In high crime areas where people will probably mess with your bike I prefer bolts. I use track nuts with a built-in washer and carry a ring wrench to tighten the bolt properly.
In lower crime areas I use QRs to save on tools and speed up repairs.
QRs are better at handling cracked axles, they hold the assembly together until you get home, but with freehubs, axle failure is almost unknown.
I find that wheel alignment is the same for either method.
Locking skewers are probably the best solution.
How tight can you get an axle bolt using an allen key?