So this is interesting.
A video has turned up online showing a secret mission in last years Metal Gear Solid: V Ground Zeroes that seems oddly prophetic. The mission is called Deja Vu and has you dressed as Metal Gear Solid 1 Snake running around finding old Metal Gear Solid game logos. As you aim at them, most of them disappear.
Except those that aren't directed by Hideo Kojima rather interestingly.
This is eerily similar to Konami's treatment of Kojima's name in recent months as they retroactively have erased his name from titles he's worked on. Also, a lot of the dialogue associated with the mission seems to be geared towards saying goodbye. Take a look at this video from:
Honestly, I think this is 'somewhat' coincidental and may have been about Kojima leaving the franchise with Metal Gear Solid V, rather than Konami as a company. Remember, Kojima was working on Silent Hills before leaving, so it seems weird to think he knew he was going and then announce a new game. Regardless, this certainly is interesting and will show up on all sort of list posts about 'the best easter eggs ever' and what not in the future I'm sure.