From High Guard (CT Book 5, pg 30):
Bay Weapons: Weapons may be mounted in bays, large areas near the skin of the ship's hull. Bays are available in 100-ton and 50-ton sizes (the size indicates the tonnage required) and must be installed during construction. The weaponry in bays is easily removed and replaced by other bay weaponry as the need arises.
One bay (regardless of size) may be installed per 1,000 tons of hull available. Tonnage not otherwise allocated to weaponry is considered available. For example, a 50,000-ton ship might be assigned a 5,000-ton type A meson gun; it may install 45 bays in addition to the major weaponry.
Weapons bays cost Cr10.000 per ton; 100-ton bays cost MCrl; 50-ton bays cost MCr0.5. They need not be assigned any specified weaponry during construction.
Weaponry installed in bays may be of five different types: meson guns, particle accelerators, energy weapons (fusion and plasma guns), repulsors, and missile racks. The bay weapons table indicates the cost for one bay weapon and its energy point requirement. The table also cross-references tech level and weapon type. The number at the intersection is the factor used for the weapon on the Universal Ship Profile. All bay weapons of the same type on a ship must be identical. Each bay weapon is a battery. Weapons installed in bays may not be allocated for turrets.
Empty weapons bays may be put to a variety of uses, such as holding small craft (airlrafts, ATVs, fighters, pinnaces, etc), or storing cargo. Vehicles and craft may be carried in otherwise unused bays at 50% wastage (100 tons of bay holds 50 tons of vehicle or craft). A bay may launch one craft per turn. An otherwise unused bay may also be used to carry deadfall ordnance for planetary bombardment; such a bay is useless in battle, but is used to bombard worlds.