I handle all of our ducklings routinely when they're in my bathtub brooder, and I can't say as though they act like they like it!
I do think it's important, though, to check them over regularly, and also to get them accustomed to being handled. Most of the animals on our small farm are here for the long term (we don't run breeding or meat operations) and so they'll need attention periodically for routine cuts and scrapes, vaccinations, foot trims etc.
So we do play with the ducklings while they're in the brooder, and try to handle them and get them accustomed to people being around. They still act like we're going to kill them every time we go near them, but it certainly hasn't made them more fearful of humans.
Personally, I've come to the conclusion that the ducks are just the drama queens of our farm-- they'll pitch a bi**ch about ANYTHING!
definitely drama queens before I knew mine were girls I named them skitzo and freud