You mean the ones like "NO STEP", "NO PUSH" and the like, right?
Just from my own observations, seems that a fair number of Army crew-chiefs and Navy/Marine plane-captains had an aversion to re-applying stencils after doing damage repairs/replacements... From my own personal experience, at unit level, there was usually only ONE stencil kit in the maintenance section, and it was usually missing half the letters & numbers... Any gear/equipment that I had to stencil (by regulation) was done with my own stencils that I'd buy, if and when I ever got around to it..
I don't know for sure, but I'd imagine that it was more difficult in an operational unit in WW2, since by my time in service, many of the stencils, rather than painted-on, were actually self-sticking labels that you'd order a hundred of to apply after repaints... But for vehicles and outside the necessary bumper numbers and the like ("FILL TO THIS LINE ONLY TO ALLOW FOR EXPANSION", "NO Smoking within XXX Feet", etc.) they may get re-painted with a nice set of stencils... Eventually...
GAWD, I remember the ONE time I did an F-4 Phantom in the SE Asia camo and applied EVERY stencil on the sheet... All that beautiful airbrushed, four-color paint, lovingly and pain-stakingly applied... Looked like it was covered in bird-crap from a short distance away...
Frankly, I'd apply a chosen few and leave the rest off to give it a little character, but not the full monty of factory stuff...