To my knowledge, neither snaking nor space flight was a problem in F-Zero Maximum Velocity (GBA) nor F-Zero X (N64)-- those games can be enjoyed straight up
For F-Zero GX, snaking and space flight presented an initial problem, as the exploits were discovered, but eventually the community moved to create separate ladders. IMO these sorts of glitches and shortcuts are unfortunate but can easily be managed by splitting the record system and appropriate oversight. The mods simply say, "there is no snaking or flying for records in this system," and require video proof for suspect times.
In some ways, glitches/shortcuts make games more interesting because there are more than one way to play them. Some shortcuts in Mario Kart and F-Zero GX are really challenging to execute-- and some people enjoy competing for fastest times using every glitch/exploit they can find. This seems perfectly reasonable to me as long as there are separate chart systems.
I think you are right-- Wipeout games are relatively "clean" in terms of exploits/glitches. Using tape to perform a controller mod would probably not be a big deal for the Mario Kart and F-Zero communities, as they seem pretty open to simple stuff that doesn't involve emulation or software modification. (Not saying this is good or bad, just point it out)