From the dialogue it sounded like the Fesarius was controlled by Balok's smaller ship and was described as a "complex". In that context it would seem that the Fesarius is composed of a bunch of Balok's ships or systems like his ship so probably not an empty shell, IMHO.
BALOK: I have no crew, Doctor. I run everything, this entire complex, from this small ship. But I miss company, conversation. Even an alien would be welcome. Perhaps one of your men for some period of time. An exchange of information, cultures.
...
BALOK: (laughs) I see. We think much alike, Captain, you and I. Now, before I bring back the Fesarius, let me show you my vessel. It is not often I have this pleasure. Yes, we're very much alike, Captain. Both proud of our ships. (Emphasis mine.)