This effect in Zelda is extra interesting when you take a look at exactly what games have toilets, and the style of the toilets themselves! Toilets show up in exactly three Zelda games, all of which have extenuating circumstances.
1. Majora's Mask (2000). Probably the most infamous of the three. Very basic style of toilet, just a hole with some wood around it: pretty much what you would expect from a fantasy toilet. I will note, it's on the second floor of the building it's found in. Kinda weird. Hand is named ??? and gives you a heart piece. Something to note is that it's found in Termina, the alternate reality/dream/country in which the game takes place. This is not Hyrule. Interesting.
2. Oracle of Ages (2001). Same style of toilet, same kind of hand. Came out a year after MM, and developed by Capcom, so it's interesting that they chose such a small gag to put in only Oracle of Ages, not its sister game, Oracle of Seasons. Also, OoA takes place in Labrynna, a different country from Hyrule. It also takes place in a different timeline from Majora's Mask.
3. Skyward Sword (2011). This one's the weirdest, and for good reason. First of all, it has WORKING PLUMBING. It flushes when you stand up. I'm not even kidding. Looks the most like an Earth toilet, complete with lid. It's found on Skyloft, which is, again, not Hyrule. The hand in the toilet in this game is named Phoeni rather than ???, following the same naming convention as the rest of Skyloft (named after a bird), thus insinuating that they are part of Skyloftian society somehow. Also note that Skyward Sword is the first game in the series chronologically, taking place before the creation of Hyrule.
So in essence, not only do people not build toilets because of the hands, they a) don't build toilets in Hyrule at ALL, b) used to have enough plumbing knowledge to make toilets flush, and c) have since lost that technology since moving to the Surface and starting Hyrule. Thus, we can build a hypothetical picture of the impacts of repeated chaos due to either war or the curse of Demise (aka the reincarnation of Ganon) on Hylian technology, assuming the disappearance of plumbing is representative of many other lost arts. This is especially interesting due to the fact that we have evidence of at least one other country with toilets (idk how y'all want to count Termina), late in the Fallen Hero timeline which is arguably the most chaotic timeline post-OoT. So really, the destruction of such technology is particularly a Hylian problem, since the style difference of SkSw and OoA toilets are different enough that the designs were unconnected.
So yes, they're probably worried about toilet hands, given that we're 3/3 on them, but they don't show up in Hyrule, and frankly they only ever come out at night so they're probably okay with it. Nah, in reality, the lack of toilets in Hyrule is probably just due to technology lost during the country's repeated struggle with the endless cycle of destruction caused by the reincarnation curse and multiple unrelated wars. Plumbing is an archeological marvel akin to sheikah tech by the time botw rolls around. Just...wayyyyyy older, and still undiscovered.
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