The Mario wiki for Yoshi Valley says:
The map modes that show the player icons making circuits around the screen relative to their positions seem to work fine; however, the maze is so complicated that determining the racers' current positions is impossible, so the players' mugshots will just be replaced with question marks.
Were question marks used instead because of a hardware limitation on the N64 itself? Meaning the N64 couldn't keep track of all the racer's positions in real time? I don't think impossible is the right wording, because the first place kart is flashing rainbow on the minimap during the race, so the game tracks the kart in first position.
Or were question marks simply used to add some more fun to the multi route track, and never knowing where you're at exactly when playing?
Best Answer
While I do not have insight into the game's code, there is evidence that there was no such hardware limitation.
This Game Screen is also available in Yoshi's Valley and works in the same way, though all player icons are now question marks as well. As you play, you can observe some players making significant jumps as they traverse shorter paths. The question marks also rotate as the players they represent get hit by items or obstacles.
Based on the evidense, it is very obvious that the Nintendo 64 is fully capable of keeping track of player positions even in Yoshi's Valley. Therefore, I believe that the question marks had nothing to do with hardware limitations, and were actually meant to add more suspense to the game, as players would have no way of knowing whether they chose the right path or not.