I have worked this out for my hybrid CT/HG system. You may find this of interest.
The first thing you have to work out is the size of the bay missiles, and what a battery shot of them means.
I worked out from both the 15cm width of the turret missile compared to 25cm of the bay missile and the relative HG battery fire that 1 bay missile is equivalent to 15 standard missiles, 750kg in missile supplement terms.
For a dirty quick build, take a high end turret missile from the missile supplement including smart, triple the smart cost to cover some armor and ECCM and PD decoys to give them greater survivability, and otherwise multiply the price x15. Warhead strength would be 15x1d6 or 15 throws 1d6.
My advanced version basically involves building a 50-ton small craft or 750-ton boat, adding in warhead costs, allowing for higher G then 6 on a sliding TL, significant fuel rate, then dividing by 1000. I use the Striker nukes for 15cm and 25cm shots, seems more in reason then the million credit plus ones.
This means that a 100-ton shot is 2 missiles each and a 50-ton shot is 1 missile. Both bays therefore have a 50 shot limit.
Of course one could have the 50-ton fire 2 missiles for a full battery shot, or 100 single shots from a 100-ton bay. Field reload of bays should be possible, but laborious and something normally done after the battle.
I grew up on Imperium, so mass dumping those missiles were always something I wanted, chafing at the single missile per launcher/turn limit.
Of course allowing that means serious imbalance in favor of missiles. So I came up with limits and counters. The lasers and energy weapons can fire a free PD round of fire in addition to main targets if powered (just like CT), and repulsor fire applies to ALL missiles coming from a single ship.
Sandcasters start looming very large if multiple missile swarms are allowed.
