You're misunderstanding the nature of the inclusion of things like hint systems. The point isn't that the puzzle can't be figured out by the average person, but that you shouldn't be restricted from enjoying the game if you can't figure a puzzle out; the option to be given a hint as to how to progress past a puzzle that "beat" you is a good one for those who want to play the game more casually. This is almost the stated goal of Nintendo, if I recall, although I can't cite it. It's not an uncommon agreement, either, and we shouldn't apply some kind of different rule for video games that doesn't exist in other modes of entertainment; when people play riddle games and one person gives a riddle for the others to solve, the others often get stumped and ask for a hint so they can have another try without outright giving up.
Anyway the very nature of puzzles requires that hints of some kind exist even if they're not hint systems of the sort you see in Zelda, because a "puzzle" that has no trail, as it were, to follow towards its solution isn't a puzzle. It's just an abstract obstacle you can only pass with a guide, trial and error, or luck. Well-designed puzzles hint towards their own solution in subtle ways. So in that way, no, hints can't ruin puzzles; hints are inherent to puzzles. Every puzzle needs hints, or "clues" as you called them later in the thread.
More obvious hints like those in Zelda hint systems are a bit different, sure, but at the end of the day, again, all they are is a system to make the game easier so getting stumped by a puzzle doesn't ruin the whole experience by barring your path. If they bother you, then you don't have to use them, in the same way that you don't have to use a strategy guide or a walkthrough just because it exists.
