I guess it depends on where you live. When I went FI / Headers, my installer/tuner advised me not to go catted (I was going to until then). I'm told that it's not a matter of IF but rather a matter of WHEN the cats would get clogged, and probably destroy the engine (if not caught right away).
I took his advice, he did the install / Dyno-tune, it runs great and has a minor objectionable odor on startup / idle only. Once it's warmed up, it has VERY LITTLE noticeable odor at idle.
I have a couple of options if I need an inspection (which I don't since I register elsewhere). I can throw the catted H-pipe on there and go get it inspected, or I can go to one of many shops around here that don't look for cats.
My O2's are NOT turned off in the tune, and I get NO codes, and NO "Not Ready" signals. He's a great tune guy.