In a multiplayer game, it is HIGHLY unlikely that number will be and remain negative for a significant amount of time.  I suspect it was a programming decision (one which may be reversed if it is found to be too abusable).  It is currently the ONLY way to get a negative fleet remaining without having cued research for more max cap (and even then you can only CUE, not build the ships in question).  While it is abusable in single player, it is generally not considered game breaking, as with the same resources needed to make a massive fleet, you could just as easily steamroll a couple of people and the moment you hit serious combat, the advantage gets neutralized.  On these grounds, I would say it's in the 'unclosable hole' category.  Allowing going a couple of ships over is intentional.  Allowing going 500 cap over is not, however, the intent, and if it is overly abused, measures will likely be put in to enforce it.