I don't see the point of a mass penalty, since OmniMechs don't gave one. Instead, I would recommend a facing limitation: each facing would have a designated amount of pod space available that is explicitly stated. For example,a WarShip with 120,000 tons of pod space has to state how many tons per arc are available -- even if the default 15,000 tons per arc (Nose, Fore-Left/Right, LBS/RBS, Aft-Left/Right, & Aft). If you want more pod space in the broadsides, you have to limit other arcs to do so.
The main problem I see is cost. WarShips are already expensive (albeit not quite as bad as the old x100 multiplier they used to have), but adding another 25% on top of that is going to make them even more expensive to build. Unless you have a lot of hulls to use, the greater flexibility of an Omni design will be diminished by the lack of available ships.