No, it's not really going to slow them down, but it will encourage the plant to bush out with more lower branches, and every side branch you cut, 2-4 more will shoot off from the apex of each leaf node to encourage sturdier growth. I highly recommend this if your plants are getting tall, but only if they have 6 or more sets of leaves. You don't want to stress out too young of a seedling with pruning, but if they are 6 inches tall or more, and have say 8 sets of leaves, it wouldn't hurt to prune a few off the top of the plant. If you exercise caution when pruning, and do it periodically when the plant gets tall for the amount of foliage it has, than there will be less stress on the plant when it finally starts fruiting. As a bonus, if fed properly after this, it will put out a lot more peppers, since there is more compact foliage growth and the plant can photosynthesize more rapidly. Another thing with that vein of introspection is that the plant becomes a lot stronger and won't become stressed trying to support heavy (comparatively speaking) fruits on a fairly tall plant.
Look at the apexes (where the leaf stem branches off the stalks), and if there are little buds forming, that's when you know that the pruning is working, since those will start to grow much more rapidly once you prune the tops of the plants. Some plants do the bushy growth all by themselves, and when pruning those, they get so bushy that it's dumbfounding to see it grow like that! I have a few C.Chinense that love doing that, as well as some C.Annuums that do it. I still pruned them, and the new leaf nodes are starting to take off fast!
