Excepting for hardpoints, which are reinforced structure within a ship to support the stresses produced by a weapon firing, everything else in the game is a balance function.
Unless there is a specific reason for that empty space, such as a vacuum serving as a firewall, no Naval Architect would follow the concept that volume in a ship goes unused.
This game tries to enforce balance against principles that are not, and cannot be, in competition. As a result, you get shipping that follows no logical design.
If I were building an unarmed explorer, as most of them are, I wouldn't be wasting huge amounts of volume with hardpoints, which is what currently happens. The volume is allocated to weapons the ship will never have, meaning that in the current system, that space is a big hole in the ship that can never be filled and serves no purpose.