i suppose it always depends on the does temperament, but I find even a nervous doe will calm down if u give her a treat away from the nest, that way you can quickly check for full bellies and that they are warm. the checking only needs to be a couple of minutes, and I handle the babies the day after my doe has them, (only for a few seconds each), for checking purposes. I think most does, if they know you well enough, do not mind their nest being checked, my Bun will just come over to check up on me and her babies when I check her kits, (as if she is making sure I am doing the right thing).
When their eyes open, or at 2 weeks I will handle them a bit more, (strokes, pick them up for a minute longer. Like Preitler I find this helps with them staying calmer at a younger age, as they can be extremely nervous at this young age, just beginning to explore. from my experience It helps in the longer run for having calmer, friendlier, more trusting bunnies.