Everything I've read suggests that they only replace the entire keyboard, or in the case of the new Macbook, the entire top half of the computer.
I've also read that the scissor switch breaks when you try to remove the keycap, so I'm not sure how replacing individual keys would work.
The big thing is the keycaps and scissor aren't designed to be removed, unlike other parts of the machine, so you will break a large fraction of the ones you try to remove, and those will need to be replaced with a new key and/or scissor. And they're small and fiddly to replace. So there's a difference between replacing 1, 2 or 3 missing or wonky keys and half the keyboard. Many shops would probably only want to replace the whole top case after a certain threshold due to the time and work involved. If the keys are sticky it's different too, since the keycap, scissor plus the part of the top case below and around the key would need to be cleaned to get it moving well. With more than a few keys this starts to be a lot of work.
The butterfly keyboards don't have replaceable mechanisms, and the keycap's tabs are so small that they are not meant to be put back on, but instead always replaced.
But this only helps with some kinds of key issues where the keycap or scissor mechanism is the problem, like sticking or rubbing keys (and dirty keys). It usually doesn't help with issues like no key response or wrong letter being typed. In this case the keyboard, and therefore the top case, would need to be replaced.