Per catalog the elements on the server are listed so you can pick the ones you need, and the ones which are used in your project are pre-checked. Hiding them is a bit odd, to be honest, as it would confuse later on when you want to include an element which is 'hidden' or 'excluded'.
If you don't alter the set of elements after a refresh/sync you don't have to pay attention to the lists at all, all used elements in your project are pre-checked.