In deadly alliance it says he found an ammulet "similar" to the one shinnok had. Who knows how many of these amulets there are...and some of the things in the game seem to be just for fun, not meant to be taken seriously or taken as a part of the storyline (like how all the enemies die was because they thought it'd be boring if they just ran away, so u kinda have to set the storyline aside to have some fun with the fatalities).
In any case, this ending seemed to be all in fun, shao kahn didn't really die, and who knows what parts of this game they will reference in the next game, not everything is set in stone just like in the endings of the other mk games where some parts they keep in the game after and some they toss out. That make any sense? lol
Whew a lot of writing there sorry I really let lose with my opinion.