Well, the
Prometheus was firmly established to have a crew of four. No real need for a Ready Room there!
Really, the ship seems to have been built in order to remove the crew from the equation. Just four people in the command section to run the show (and indeed just four people in the entire Starfleet trained to operate that command section!), and then two mighty droneships to do the actual fighting. A logical compromise between the dangers of letting an M-5 control everything, and the immorality of sending innocent young humanoids in harm's way.
It would make little sense to provide the interiors of the droneships with anything beyond the most basic access tunnels, as there would be few mission types where those sections would carry crew or passengers. The upper drone seems to carry the ship's shuttlebay, though, so one might postulate shuttle maintenance shops and perhaps Marine barracks there, too.
The command section might have facilities for alternate "conventional" starship operations, but the prototype vessel probably wouldn't be equipped for those yet. The sickbay appears fully automated, although later on it might be provided with live medical personnel for "extended operations", and with capacity for more than four people. Similarly, there might be a galley waiting for the cooks and their ovens to come aboard, sonic shower stalls that don't have any sonic showers installed yet, and so forth.
On the aft torpedo tube issue, a drone swarm might not really need one. One drone's forward tube could be covering another's rear arc.
(Welcome back to active status, BTW! That's what summer holidays are for...

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Timo Saloniemi