Adonis of Ensemble Stars! thinks of himself as scary-looking and intimidating, and is generally very humble about himself, but he's incredibly kind, hard-working, and honest, making him unknowingly very charming. A common scene has Kaoru wanting to flirt with girls, only to see them all crowded around an oblivious Adonis. In one instantly famous scene, Adonis tells the player character that he wants to help her whenever possible because he loves her (using 'aishiteru', a very strong way to say 'I love you' in Japanese). When Anzu is immediately very flustered, he reacts with confusion - after all, he sings lyrics like that all the time on stage, so why would it be different in person?
Kaze, according to his support conversations. Several of them feature him getting saddled with gifts from random women, and he's completely baffled each time. Corrin even hangs a bit of a lampshade on it in their supports.
That's rather funny, given that Corrin himself is one! His best friend Azura, his maid Felicia, Hinoka, Sakura, Camilla, and Rhajat are all either suggested to or outright stated to have felt some sort of attraction to him before the possible Relationship Upgrade. Sure, the first four don't really make any moves, but Camilla and Rhajat are very obvious about their interest in him.
Katalina of Granblue Fantasy. Despite attracting several admirers of both genders (Vira, Lowain, and Farrah to name a few), she's totally unaware of it.
King's Quest's Alexander is a gentlemanly Tall, Dark, and HandsomePrince Charming, who is often described as good-looking or even beautiful, and frequently has women (even non-human ones) gushing over/flirting with him. But he reacts to the attention with genuine embarrassment, bewilderment, and/or self-depreciation, as while he recognizes their interest he doesn't understand why, as he doesn't think he's anything special. And when he falls in love himself, he worries incessantly that the girl won't find him attractive/appealing.
When Link isn't depicted as a flat-out Chaste Hero, he's sometimes depicted as being receptive of female attention but unable to detect any sort of romantic element in it (even though said element is painfully obvious to the player).
Justified in the case of Ocarina of Time Link, since he's a kid. A kid who grew up with no adults around at all. No parents, no nothing. Taken a little further in the manga version, where Ruto outright proposes to him and he doesn't know what 'engagement' means. And he never really got the chance to learn about romance when he got older, given that he was in stasis.
So far, the only real subversion is the Link of Skyward Sword who, while still a Heroic Mime, seems to have a much closer and personal relationship with Zelda than any other Link has had with any girl. Rescuing Zelda is his main goal rather than just saving the world.
Mass Effect: Andromeda: Jaal manages to combine this with just being a regular Chick Magnet. A background conversation on Aya has another angara complaining how he didn't notice her attempts to flirt with him... which is pretty impressive given the angara are all about honesty.
In Octopath Traveler, resident scholar Cyrus has been noted to be a very handsome teacher who has charmed many female students. Unfortunately for every girl concerned, Cyrus only ever cares about his teachings but has absolutely no idea about their infatuation for him, and it only gets worse when he freely describes women as gorgeous and beautiful... as facts, not compliments. This trait of his leads to the headmaster banning him from teaching because one of his infatuated students spread a rumor that he was romantically involved with the princess of the kingdom. Throughout his story, this becomes a point of hilarity to the player and anyone else who knows about his infamous reputation as a lady charmer. Even the Big Bad was subtly flirting with him but grew sick of the long speech of his ideals to share knowledge to the world instead of keeping it all for themselves.
He even manages to charm Primrose, a woman who is literally a professional at seducing people and remarks that she can't tell if he is trolling or if he is sincerely, genuinely guileless and does not understand how attractive his Gentleman and a Scholar demeanour is and the kind of signals he continually gives other women.
Mario in Paper Mario: The Thousand-Year Door. There's the obligatory implied romance with Princess Peach, but beyond that, every single one of his female party members develops a romantic interest in him. Random female NPCs will also flirt with him in their dialogue and even one of the baddies admits she finds him handsome. That said, he seems genuinely shocked when Flurrie and especially when Ms. Mowz flirt openly with him.
Tatsuya Suou. The boy is absolutely oblivious to the affections of his childhood friend Lisa Silverman — who he sees more as a Clingy Jealous Girl. His cop brother's Katsuya not exempt from this, either. This even while they are both head-over-heels with MayaAmano.
How dense is Katsuya? One time, on Valentine's Day, a female cop gave him some chocolate. In his capacity as an amateur chef, he spent a while telling her everything that was wrong with the chocolate, from texture to flavor and asking why he was getting it since it isn't his birthday.
Shenmue: Ryo Hazuki blows all other competition out of the water in this regard. He could practically receive a concussion from all the girls beating him over the head with their attraction to him, and he just. Doesn't. Get it. Supplemental materials explain that Ryo is both preoccupied with getting revenge and deliberately averse to female attention because of a rough experience in his childhood, but this doesn't come across that well in either dub, making it look like it all simply goes in one ear and out the other.
Both Lloyd Bannings and Rean Schwarzer in the Trails Series have a number of women who would throw themselves at them in their respective arcs. Despite all that, however, the two protagonists don't see it themselves. Just to drive home the point, Rean currently has 12 girls who are romantically interested in him. Millium is the only main female party member who ISN'T an option, but she was one in the first games.
Hyde Kido of Under Night In-Birth has a ton of different cute girls in his life, and he is completely useless with all of them. In fact, his interactions with women tend to be played for comedy more than anything. He keeps Linne and Vatista as Pretty Freeloaders in his house, doesn't realise Orie has a really strong crush on him, doesn't realise his old childhood friend Yuzuriha doesn't actually hate him as he believes, and he's the only person in the game who gets duped by Hilda's Femme Fatale act by virtue of being a horny teenager.
This comes up again in his depiction in Blazblue Cross Tag Battle, where most of his unfortunate moments come from dealing with the female characters of the cast. He gets dragged into a fight against Chie and Yosuke by Ruby, he rescues Weiss when she's being attacked by Azrael and Carmine only to get snarked at for his trouble, then he gets ambushed by Blake and Makoto and Gordeau has to bail him out, then he meets Yukiko and has to fight Noel and Platinum and has to eat Noel's lethal curry if he loses. Poor guy.
Aoife in Valkyria Chronicles 4 is a Gender Inverted example. She's so beautiful and sweet, with a habit of paying well-intentioned compliments to the men in her unit, that she has a huge throng of admirers who think they have a chance with her... and she is completely unaware of it. Her Squad Story is all about one of her squadmates trying to work up the nerve to confess his feelings, only to find out that she already has a fiancee, and all of the things that others mistook for affection were simply because she is very nice. One of her female squadmates ends up astonished by how much of an 'unintentional seductress' she is.
The titular character in Wadanohara is oblivious that she is being crushed on Samekichi, Fukami, and Sal for most of the game, and ultimately ends up with Samekichi in the Golden Ending after she gets the hint.
Since Yandere Simulator will be a 10-week long game with a new rival each week, this means that Senpai has, completely by accident, managed to attract the attention of 11 different girls. And Word of God is that Removing The Rivals by setting them up with other students will have him come to believe he's just not attractive.