So long as your pokémon gives you consent in this sort of situation (and most pokémon can), it’s actually not considered abuse, although admittedly, there is a bit of discussion in certain pokémon professional circles over whether or not a pokémon would fully understand what body modification entails. (Strangely, yes, this is a common enough question for there to be a debate. It’s just that I normally hear this question asked regarding fighting-type pokémon and tattoos or, bizarrely enough, pikachu and spiked fur.) Personally, I believe that so long as the pokémon and piercer or artist are fully consenting to working with one another and so long as the methods used are, well, legitimate, it’s perfectly fine to help your pokémon modify its body in whatever way it wishes. The professional body modification community evidently feels the same way, as there are plenty of people willing to modify pokémon if you know where to look. They aren’t nearly as common human-only tattoo parlors or so forth because of the above-mentioned debate, but they’re there.
As for the risk of infection, actually, no. Poison-types are generally immune to their own poisons, and if anything, their poisons can actually be a disinfectant, as, well, it can be toxic to bacteria too. Alternatively, some poison-types are symbiotic with powerful strains of bacteria (such as in the case of trubbish, one of the few such pokémon capable of being modified) and thus wouldn’t actually feel much in the way of an effect there. If anything, piercing a nidorino or any other poison-type may pose more of a danger to the piercer, as there’s a chance that the piercer could be exposed to either toxins or bacteria or both as part of the pokémon’s natural defense mechanisms. This goes doubly if your nidorino’s ability is Poison Point. However, if you take your nidorino to an experienced piercer who’s worked with pokémon before, they should know how to avoid a nidorino’s quills.