Considering there was no joint Konami/Silicon Knights/Nintendo remake of Silent Hill, I would say it's unlikely that MGS1 isn't included because Nintendo has the rights to Twin Snakes, thought they may indeed own portions of what Twin Snakes contains. Being PSX games is the big thing those two games have in common.
In any event, as great as it is that they're rereleasing these old games as HD ports, I would've loved to have seen 'GCN Resident Evil calibur' remakes of MGS (with MGS4 or greater graphics) and Silent Hill (SH5 graphics) but yeah, it's far easier to just port stuff with better textures. Then again, we kind of DID get MGS1 in MGS4 graphics already.