Not from Kojima himself, but in the confusion ensuing from Kojima's leaving Konami's board of directors/the company as a whole, Konami opted to remove his name from his own products as a response; the outcry from fans saw Konami abandon this initiative.
Since his name was successfully scrubbed from the box art for Metal Gear Solid V: The Phantom Pain, there has been a wave of people on the Steam review page leaving a single message for their review; "A Hideo Kojima game". There was even an "unboxing" which consisted solely of putting Kojima's name back in its rightful place, all while "The Best is Yet to Come" plays.
Kojima himself thanking the fans for everything and for staying with him through and through.
The fan dedication at the end of that video, to an adoring fan who unfortunately passed away prior to Phantom Pain's release, is truly touching; Kojima clearly understands the chords his series has struck with his fans and appreciates that they've allowed him to come this far.
Despite Konami's controversial decision to give the award of Metal Gear Solid V: The Phantom Pain to a PR representative, both Kiefer Sutherland accepted his award in his honor, and Stefanie Joosten deciding to sing Quiet's Song for him.
E3 2016, specifically the YouTube at E3 stream hosted by Geoff Keighley, who happens to be an old friend of Kojima. The hug at the beginning of the interview, the personal invitation to the Game Awards and the gift of Kojima Productions merchandise he gave to Keighley.
During Sony's E3 presentation, Kojima literally walks down the stage under stairs of light, and cements his introduction with two words: "I'm Back." The reception to his return was a sight to behold. Kojima himself was so excited that he flubbed his entrance, and ended up overtaking the lights he was supposed to walk on. He also seemed rather overwhelmed and touched by the sheer magnitude of cheering his entrance received.
Finally in the 2016 Game Awards, after all his troubles last year with Konami banning him from even attending the 2015 one, Hideo Kojima is presented the Industry Icon Award. See it here.
Related to this, Geoff Keighley had spent most of the past year doing whatever he could to try and give Hideo his award for Metal Gear Solid V.
More at the fact that Hideo kept insisting to Geoff not to, because to him it wasn't necessary. And yet Geoff insisted and right on that night, Hideo accepted the award and even came close to Manly Tears, especially when he gently talked about how he felt he had almost lost everything.
Shinji Hirano, former president Konami Europe, went on to Kojima's side, becoming an acting president of his company. It says a lot when a former Konami president chose to side with Kojima.