Kevin was succinct, but to elaborate if I understand properly:
Transports by themselves, never block enemy movements. This means yes, you can have one ship move into the transport sea zone during combat moves and send other ships through that zone to other zones during combat moves. Or you can ignore the transport and move through it during non combat moves.
Remember, killing a transport is a naval battle in that zone. This will prevent any coastal bombardments from that zone as a naval battle existed.