I think that (if you really wanted to rationalize this) you'd have to explain the large external weapons by
A) the designers didnt have the internal space to put a weapon... the lasers on the Hornet are almost as long as the craft itself, so to keep the ship as small as the did they would need every bit of internal space for fuel and powerplant.
B) the weapon designs hadnt progressed enough that they COULD fit them into a ship's hull. As technology progresses it tends to get smaller and more efficient, but initially it is large and bulky (and fragile). Witness the evolution of the armaments of the Rapier from WC1 to WC2. While still visible, the weapons are noticeably smaller for the same firepower. Also witness the massdrivers - they go from the i-will-impale-you attachments of the Scim to the little cheek pods on the Ferrret. Your tax dollars at work...
Two other things to keep in mind - there was the major design philosophy change from WC2 to WC3. It seems that the techs recognized the value of internalizing everything and armoring over it all, creating a much more survivable (especially in terms of spare parts!) craft. However, the space allocated to the weapons (prime example: dorsal and ventral weapons boxes on the Longbow) is still significant, taking in mind that the ships of this era are larger than their earlier cousins.
Finally, for Preacher: yes, the long barrels ache to be snapped off. Seemed that happened every time the shields on my Hornet went down in fact... however, there is a purpose. Until the weapons were miniaturized, the longer barrels would have provided a better bottling and focusing for the laser, and a longer acceleration run for the massdriver.