No. The buses will still be running to Downtown Disney. The system shuts down gradually throughout the evening. As the first park closes (usually AK) the buses service that park until it is empty, or about an hour after that park closes. The same for the next park to close, and so on.
Buses continue to operate between the resorts and Downtown Disney's three stops until late into the night.
The Marketplace stores close at 11:00, so buses stop going through Marketplace at about midnight. The buses continue to operate from Pleasure Island until 2:00 AM, and sometimes a bit beyond that.