How can I finish off a three gang switch with one switch missing?
I can't speak to the codes portion of your question, however my husband has been changing out our builder's outlets to z-wave since we moved in.

As long as your wires are capped off (I'll assume tapped off is the same thing) how about putting on a 3-gang switch plate with 1 blocked?

Hubs did this recently with a 2-gang. It leaves all the wires accessible behind the plate should you need/want access to them for a future project while still closing off/shutting down the area that's not longer in use.