Well, all of them presumably. All the command droids shut down when the command ship did.
And in answer to your other point, this is IN TPM, Yerssot. The fleet leaves the control ship. There were droids on the ships that left- lots of them. Including ones operating the ship and providing security. They presumably would have to work without the control ship or they would all turn off when they left the blockade.
I think I get it now; do you mean at the start of the invasion? The big schips that land on Naboo, and the commander saying than "If they're down here sir, we'll find them"?
I think that they are divided into sections, so you can turn section 1 on and the other 500 aren't active. The button used for the battledroids ("Activat the droids"😉 is maybe the main-button?
Very strange, thanx for pointing that out Ush