The accepted practice is to use track nuts for fixies. I use track nuts on my track bike, but since the 70's, I've always used QR's on any road fixie I've ridden. Yes, you're more likely to pull a rear wheel secured with a QR, but at least it's a lot faster to straighten the wheel if it's got a QR. And I've pulled wheels with track nuts as well, but you're likely to be exerting more instantaneous forces on the track than you would on, say climbing a steep hill on a fixie, anyway.
Yes, wheel theft is a concern, but when I lock my bike to a rack, I usually remove the front wheel anyway and put the U-lock thru the rear wheel and seat tube and then around the front rim. In the winter, I'm using a fork with a disc brake attached (I've broken too many front rims from brake track wear), so I haven't filed off the lawyer tabs, which means I have to turn the acorn nut anyway, so it's probably just as slow as using track nuts, but then at least I don't have to go searching in the seat bag for the wrench. In the summer, I'm on the ENVE fork with standard caliper brakes, so the lawyer tabs are filed off and front wheel removal is way faster.
I also usually carry the fixie in the trunk of my car (rather than on the roof rack) if I need to drive anywhere, which means removing both wheels. It's bad enough having to take off the raceblade fenders, so simplifying wheel removal is fine with me.
Anytime I buy a new rear wheel for the fixie, I usually have to remove the track axle and replace it with a road axle with QR. Unless you go to swap meets and find old 120mm Campag or Dura Ace rear hubs with QR's, you're pretty well stuck with modifying track hubs. But I think the effort is worth it. You never want to be out in the middle of nowhere with a flat, and then realize you left the peanut butter wrench on the workstand.
But usually, I'm converting rear wheels to fixed by just pulling the Shimano cassette and replacing it with a Surly Fixxer, then shortening the axle to fit the 120mm spacing on my track ends.
If you're using a converted road bike, a big issue is rear axle spacing. You're best running 120mm spacing; it's a more symmetrical rear wheel, rear track wheels are spaced at 120mm, so there's no chainline issue, and any axle longer than 120mm is going to break on the freewheel side. That's why they went to cassettes - too many 126mm axles breaking.
It's mostly a matter of personal style, but I've always preferred QR's to track nuts. In fact - and I've been racing & training on the track for over 40 years - I've never understood why track bikes are required to use track nuts. I've never come close to being able to flip anyone's QR on the road with my front wheel! (I think it would be far more likely for me to cut someone's rear tire with the rotor of my front disc brake!) And I suspect people use track nuts on the street just because of this track bike association. I guess it's one of those things people just never question. Same as lock rings - I've never used lock rings, but I was coached from an early age that trackies must never apply back pressure to slow down; it's too sudden for the rider on your wheel and it's bad for the legs. Just one of those things I've never questioned...
Luis