I would touch my tank if there are babies. But if I do, I get a second bucket/ container and let my trimmings in the bucket for and hour or so to double check no babies cought up. For some reason my baby shrimps tend to hang on the stuff your going to pull out from the tank instead of just running away.
Especially with net, I found one tiny baby shrimp dried up when I just looking at my net in the storage :/
it all depends on the amount of plants, thickness of the substrate, amount of substrate you are going to disturb and the overall size of the tank. if you are going to prune and replant a small corner of a 40g breeder, id say go for it and make sure to check for hitchhikers. If you were working with a 4 gallon nano tank, that would be a different story.
If you're willing to sac a couple of babies, then go for it. I find that babies are extremely sensitive to environment changes for CRS anyways. If it's neos then I'd say do whatever you want as they're hardy as ants. Just don't disturb the substrate too much like many have said, it might cause an ammonia spike.