Personally, I think S.K.I.N. is disbanded, but no one's said it has been so it's more of an informal "everyone wandering away" disbandment rather than an announced or openly dramatic disbandment. (Disbandments are kind of like divorces IMO: some are handled quietly away from everything, others are explosions of high drama)
I think the primary goal of it, whatever it was, has been accomplished, everyone is far more successful in their solo careers, Yoshiki and Sugizo and Miyavi are still all working together/are friends, Gackt is off doing his own thing, and everyone's moved on and is happy having done so.
That said, if you're one for rumors, there were quite a few of some major behind-the-scenes drama between Yoshiki and Gackt. Ego clashes, style differences, something to do with Miyavi, take your pick. I'd honestly agree with these rumors due to Yoshiki's picking TMR over Gackt for the Muteki Band. . .