When he sends out his private army, we see a fighter launch from an airstrip. It is clearly a Su-27 derivative, which must have been purchased clandestinely. Learning Russian is highly unusual for Japanese people despite the countries neighbouring each other; the most likely reason for Haruka having learned it is that she is being groomed for business dealings with her father's arms suppliers.
Going on that previous point about speaking Russian, note that there is only one (villainous) party in fictional 2009 that has control of all of Russia: the Ultranationalists.
Almost every time that Nobunaga sees Yuuto doing otaku things he mentions Haruka in some way, most notably when he sees Yuuto in episode one of season two and says "You two have fun."
All the clues are there for him to be able to figure it out. His best friend, who refused anything but cursory glances at otaku-related things, suddenly starts going to Akihabara and comiket at the same time as he starts hanging around with a girl. When the comiket guidebook fell out of Haruka's bag even those who believed the book was Yuuto's still knew that it was in her bag.
Nobunaga probably hasn't mentioned it because he realizes that doing so would cause trouble, he also probably thinks that Haruka will succeed where he failed... getting Yuuto interested in Otaku culture.
Main heroine's first name starts with "Haru". Brown hair and eyes. Accompanied of a Rei Ayanami clone. "Family-Name Given-Name (no) Concept" title style. Novels adapted into two Thirteen Episode Anime series. Dancing credits.
- You know, for a WMG point, it could be valid and could have happened, but you're immediately suggesting that the author, Yusaku Igarashi, totally based his story in Tanigawa's work, and such statement is as ambiguous as it gets. In that case all authors after Tanigawa must have taken a look at its novels for having written novels with "similar titles", or having female main characters, or having said characters with similar names (does that mean Tanigawa "took a look" at Hiro Mashima's works for naming his lead character like Haru Glory then?) or putting ribbons on the heads or wristbands on the arms or said leads, or having friends with fox-like grins and closed eyes, or having Moe full-breasted females as friends, so yeah.
- Although to be honest, NogiHaru's illustrator and author are known for not being very creative (more info on this series YMMV page) so that idea may have something to do with the similarities; the point I want to make clear is that a statement like this would be giving the Haruhi work too much credit for a series of novels that aren't even ten years old. Bottom line: "Anime Adapted Novel" is not a synonim for "Haruhi", neither is Tanigawa's work a synonim for the former fact.