score:4
The last Line 1 metro leaves Piraeus at 00:15, so you're cutting it awfully close even if your ferry arrives precisely on time, and it doesn't pass very close to your hotel anyway (you'd need to transfer to Line 2).
Bus 040 from the port to Syntagma (near your hotel) runs every 30 min through the night, so it's probably a better bet.
As for the hotel, you should get in touch with them and make sure they understand you will be arriving very late, so they need to keep your room.