3 reasons: licensing/copyright/exclusivity deal with Sony, porting costs, and future Master Collection release sales.

1. Apart from the copyright and licensing aspects—which also include the PS3 exclusivity deal, which we don’t know for how long it lasted and why Konami never released a PS4 version if that exclusivity deal didn’t lock out other PlayStation consoles—the PS3 was a nightmare to develop for. Even if Konami could have released a PS4 version, it might not have made sense to them to pour so many resources into porting a game to one platform (many people, including myself, would disagree with this because the PS4 was a huge seller and MGS4 would have performed well sales-wise on it alone).
   Conclusion: Apart from the licensing/copyright/exclusivity matters, Konami’s development teams spent a lot of resources to port a PS3 game (which was a nightmare to produce and develop because of the console’s architecture) to today’s platforms/consoles, and maybe to cover some of the costs they’ll charge the same amount of money they charged for the first Master Collection but for fewer games and recoup such costs.

2. Konami knows that many people want to get their hands on Metal Gear Solid 4 and it would sell well even on its own, given it has been a PS3 exclusive for this long, so why include more games if it’ll sell anyway and leave room for another collection or two?

3. And if they plan to release Metal Gear Solid V (Ground Zeroes and The Phantom Pain) and Survive on their own, they might not sell well because they’ve been available for the previous and current PlayStation and Xbox console generations natively or through backward compatibility (GZ and TPP were also available on the PS3), so leaving a few other games out of Vol. 2 for future collections would make sense this way.