True, but I think it's value as a collectors item decreases based on its general feeling as a rarity. The GameCube was an underselling console, and the physical copy of Metroid Prime was the only way to play the game. With this in mind, and as copies get lost, damaged, etc, it's value as a collectors item goes up, even if technically it's sealed and not for playing. Its value also competes with players that do buy the copy and unseal it to play, which most players up until now did since that was the only way you'd experience the game (I don't think emulation has much of an effect.)

Plus, Metroid Prime for GameCube is already a valuable collectors item, so I don't see the remastered version with a digital release matching it's value.

Rarity is just one aspect of its value as a collectible. People have to WANT it, too.

I'm purely talking from the perspective of value as a collectors item. Sure, the physical copies will be less common, but it's overall rarity as an item will be lower due to the fact that so many more people own the game digitally. Physical copies got lost, damaged, thrown away, sold, but those were the only way to play the game (emulation clearly has no effect on collectors value.) Can't do that with digital, even if the shops themselves go down.

Keep in mind that GC was the last generation before digital releases though...,of course it's valuable when it's the only way to play/own the game for that console