Im thinking about getting into speed running and i am wondering what the consensus would be on replacing JUST the thermal paste on a switch since it helps remove some lag from games like LoZ: BoTW. Would that be considered "too much hardware modding" or just replacing a part?

Console modding isnt allowed. Plus you really dont want to do that anyway. Theres a technique that abuse lag

Alright, but the replacement of thermal paste isn't a modding thing. It's a general upkeep thing. As a matter of fact, it is good practice to keep up with thermal paste on any system that requires cooling. Doing so can greatly increase the lifespan of your device and protect the CPU from overheating. I would argue that replacing thermal paste is the equivalent of replacing a faulty fan or card reader in your device. It's not modding since the console came with the feature to begin with. All you're actually doing is putting something that should be somewhere where it belongs. At that point, I'd argue that not allowing people to do this gives an unfair advantage to those who purchase newer Nintendo Switches. TL;DR Advocating against proper practice for upkeeping your electronics is a dangerous game and sacrificing your system should never be a requirement for a game or category.

if it would be a simple piece replacement i wouldnt see a problem. However i see one if it actually gives an advantage to the runner if the console perform better because of a better piece. Plus like i pointed out some categories use a trick called "Super Laucnhes" which requires in game lag to work. Reducing lag would make this trick near impossible

Honestly, the danger of breaking something while opening your switch with the required 3rd party tools is a lot higher than keeping the factory applied thermal paste on it, so that argument is kinda void.