The ship doesn't just magically change it's setup. It moves the guns like an elevator, so it takes time. While moving, the gun can't fire. That said, the hull of the ship not interfering with the guns is really stupid -_- It would be a natural balancing mechanic if, when you put a wide arc gun on a space with a lot of clutter around it, you get limited firing arcs. It would have made SENSE. Shooting through your own hull just annoys me as it breaks all sorts of natural laws.
That said, firing 3 guns at once will always mean you either can't repair, or can't fly. The 3 guns to the rear requires the enemy to be behind thet ship, and also means it will take a while for whoever is shooting to switch to the front guns to adapt if someone comes from a different direction. The Mobula can fire four guns in one direction easier and without moving everyone far away from the hull and balloon, which are both on the totally opposite end of the ship.
A few other things to consider: this ship is relatively fragile and slow, and has a relatively weak hull. It has decent armor, but as soon as that is taken out this ship can die very fast. If you manage to get to a position where it's not focusing it's guns, it could take upwards of 6-10 seconds for it to readjust to bring more guns to that spot, and the ship has below average turning capability so it can't just turn to fix it (or it will now at least ;p).
Lets use a few example setups to show the strengths and weaknesses of the ship. Using the default setup (3 back, 1 foward and to either side) the obvious first weakness is anything not chasing you is facing a Goldfish. A slow, hard to repair Goldfish. Anything that gets behind this ship will take a pounding. Anything that gets anywhere else will do the pounding.
1 back, 2 to either side, and 1 foward: forward and back fire power is obviously weak, but it's capable of broad-siding to either side just as well as a junker. Overall this one doesn't have as many weaknesses. The first that comes to mind is if anything gets behind it, the ship is obviously more vulnerable there now. Depending on which of the two centered guns is pointing forward, and which is pointing back, either side could be more or less dangerous. Obviously this setup means no one side has a great deal of focused firepower on it as it's more spread out. This setup also has no one near the balloon, so repairing the balloon could take longer, or make the hull vulnerable by drawing the main engineer away from it.
3 back, and 3 forward: this setup obviously has great forward and back fire power. While charging, you can fire with the medium guns and both the forward side guns and deal a lot of damage. And anything that gets to the side will probably kill you before you can counter it. Now, if you move the two back side guns to below deck so they fire to either side, that just creates a reversed super-Goldfish with 3 still relatively weak sides, and no medium weapon to make that third side still kinda dangerous. Also, switching to any of the other guns means not firing the three forward guns. The obvious advantage to this is all 3 on the guns are right next to the balloon, so it's easily fixed. The obvious downside is no one is near the hull. While it's easier to get to the hull from here, that then takes one of the guns out of the equation, weakening the firepower of the ship.
While this doesn't cover all of the possible (and likely) configurations, it does cover most of the ones I see as potentially problematic. While it IS technically possible to get 4 guns pointing forward or backward, firing 4 guns at once is generally not worth the downsides, and really you could just take the Mobula and get the same effect easier. Also, the 4th gun is always going to have things in the way of it seeing what it's aiming at in one direction (and assuming the actual hull of the ship stops guns, perhaps it can't even fire in those directions). I don't see this particular setup as an actual problem worth covering more though.
EDIT: I may consider removing the medium gun in favor of a light gun, but I haven't decided yet. I'll be considering the implications this change would have.