Kojima always states a loyalty to his "Long term" fan base rather than any specific system. He asumes that most fans of MGS, which previously appeared on Sony Systems primarily, will keep buying Sony Systems, if for no other reason than they expect Metal Gear Games to keep coming out on them. If he were going to change systems my guess is he would tell his "loyal fan base" from the get go, at least, that's what he claims he would do.
Also, the 360 isn't doing so great in Japan, still, and the triumph of Blu-Ray over HD has increased PS3 sales immensely. That and the PS3/MGS4 Bundle is almost a garaunteed system seller. A 360 Version at this point is extremely unlikely, the best 360 fans will get is a "MGS2 Substance" style port about a year or two later.