Because, all the Fs2 capital ships have turret pointed to 90 degrees and so I don't really understand the reason.
That's currently a limitation of the Freespace Engine. All multi-part turret barrels (arms) MUST point directly up or directly down. Its one of the most annyong limitations that MODers have to work within. Basically, if you want your multi-part turret to be able to fire at 90 degrees offset from the barrels in one direction, it MUST be able to do the same in any direction. Basically, set the fof to 180, and you'll have to live with any firing through the hull that occurs.
Now, some time ago, Bobbeau added some code to prevent weapons firing through any model or submodel that they're attatched to, but it had to be removed, as it broke some missions. In FS2 "Feint, Parry, Reposite", the one when the Collossus takes out the Repulse, the Collossus is scripted to fire its main beams on the Repulse, but it ends up firing through its own hull partially, so the mission wasn't working properly, and the code was removed. Its been suggested from time to time, that this code might be reintroduced, but by flag only, in the ships table. That way, it would only be activated on models that experience weapons firing though the hull often, for mods.
Also, WMC recently posted some WIP code for viewing, in the SCP forum, about how to possibly get non-vertical multi-part turrets enabled, but there's no guarentee that it would work. He just posted it up incase anyone had any ideas to overcome some problems he was encountering (IIRC).