I topped some Hungarian Hot Wax last year that were getting a bit tall for my grow lights and were setting buds early. I just cut them off a bit above a leaf node where I wanted them to branch out. I think they put out two growing shoots (one from each leaf node where I cut them), which effectively knocked them back by 2 or 3 weeks, which is what I wanted. I don't think it had any impact on the final results planted outdoors.

Chiles are much like other plants and react the same to pruning.

Once a pepper is mature, its damned near impossible to kill it from mechanical damage. I cut mine back into bonsai for overwintering, and that pretty much means I hack them back to just the stem a couple inches tall. I'm fairly convinced I could cut them back to the GROUND and they would grow back (I may try that this year, it could make for some interesting bonsai).

But yeah, if your plants are getting too tall, feel free to top them. It'll force them to bush out more, but it won't do any last damage to your plants.