Thats sorta where I wonder as the submarines are really just "tracked" as a small entry of data. It might be something technical as I know the DB they use is prone to HUGE levels of upkeep needed (see housing server not being available) and yeah really just I think it would remove the "ghost houses" that are strictly there for the purpose of having a submarine bay as most the submillionaires would likely consolidate their workshops into their most valuable property they own. Especially if you limited people to 1 FC per world.
However I DO wonder how often that limit is a problem. I understand the reason you can have more then 1 FC on a world is to consider that someones alt might be preserving a FC for when members return; but I do wonder how much of a issue that is.