Not an expert on how they do it, but I've played a few. The logic in these things is excellent, they won't ever give you an unsolvable game (and the Zelda ones have been playtested to death at this point). I think they just specify the prerequisites for each item and then just don't assign them if they are impossible to get, not sure how exactly the algorithm works but I can think some easy ways on how solve this problem once you have that list of dependencies.

You can still get the wrong items in the temple of course, it just means it's outside the temple. Sometimes you even have to go into a temple you can't beat, get an item from a chest, which allows you to get the required item outside, which then finally allows you to beat it.