Question #1. If a honey super is full, and completely capped, is appropriate to harvest the honey now or is there a reason to wait and do all the supers at once later?
Yes, it sounds good :P
If one super is capped it is better stay in hives warm. In cool place it may crystallisize.
It is difficult to exctract one or two super, because you loose a lot honey to get system dirty.
Question #2. If the hive is really busy and full of bees when we take the supers off, will it be overcrowded with the removal of the supers? Where do they all go? Do I put another empty super back on ? Or is there a natural reduction of bee population and overcrowding is not a problem?
When you take honey off and honey flow continues it is necassary to give at once new room for nectar. If you have one capped box you need 2 box more where they dry up nectar.
If you do not give room enough hive will swarm.
It is good to give box of foundantions. They draw up it quickly.
And if hive is full of bees, give to it at least 2 new boxes.
Put those new boxes between brood and honey. Look brood if they are making queen cells.
If you have in brood box capped honey frames, lift them to uppermost box. If there is some brood, let them emerge.