Capships don't have shields in FS2, do they? I wouldn't know, *poke Knight Templar*

Anyway, for unshielded ships, superjuggernauts are a fantastically bad idea. You've got a substantial portion of your firepower, funds, and personnel tied up in a single ship which can be destroyed by a group of ships that cost probably less than 1% to build (you could just hit it with a cruiser sized nuclear missile, there's no way a ship that big could dodge or spoof the missile, and there's no way in hell it could survive the blast).
For universes which have capship shielding technology (Star Wars is a good example), you could argue that bigger is always better, and here's why: When you double the size of the ship, it's volume doubles, but it's surface area doesn't. So you have more and more powerful shields protecting relatively less and less surface area the bigger the ship is. To return to my case in point, that could explain why an X-Wing can't take a single hit from a TIE, but the shields on the ISDs didn't start failing until 30 minutes into the Battle of Endor, and the first Death Star's shields could absorb the impact of superheated debris from Alderaan traveling at ridiculous speeds.
So, it really depends. If you're talking about Freespace, then huge uberships are dumb (but still cool to look at IMO

), but if you're talking about Star Wars, then they make sense.