The cavity in the secondary hull may or may not be a shuttlebay. It lacks doors, and the only time it has had that blue "forcefield" glow that might indicate airtightness was for NCC-2000 in ST6:TUC.
Perhaps the space originally held some vital transwarp gear, and this was ripped out when it failed to meet specs, and the cavity was put to some other use. After all, we never see what is in this space in NX-2000; the camera only hits this spot when the ship becomes NCC-2000, several years later.
That weird thing looks like it is meant to clamp something (those aircraft landing strut greeblies). Might be towing hardware, or a means to carry heavy assault barges. Or then the ship is equipped for self-repair, and this thing unfolds to become the vessel's very own spacedock.
Doesn't look like the thing is intended to ever fly out of that cavity; it's rather too well integrated to the support structures of the cavity for that.
I wonder if the CGI Excelsiors
have anything comparable in there?