Lol. Of course Kojima won't work on a Silent Hill, it's not his franchise, why would he? The man is free to do whatever the hell he wants why would he take someone elses creation and spend 3 years slaving away on it? Would you do it in his place? It doesn't make any sense tbh, there's no history between Kojima and the Silent Hill franchise except for the PT teaser.
I'm not even sure he is familiar with anything Silent Hill except for the movies.
He hasn't tweeted anything related to the franchise, he's not friends with anybody from Team Silent as far as the public knowledge is concerned, he never even praised a Silent Hill game. There's literally nothing that ties Kojima to it.
So if there's a horror game from Kojima you can be damn sure it's his original creation