What if certain vessels came with the ability to accept these pods? Perhaps vessels in the nebula vein (modulaar light cruiser) and the Luna (wich I would classifiy as a destroyer in size). And maybe even future vessels yet to be released.
The precedent I am using for the most part is the Nebula, it had 3 variants that included auxiliary nacells, extra weapons, and the familliar sensors pod.
I propose the following.....
Additional mission specific ship equipment equipable in a specific slot or "docking port".
These could come in various qualitys and could function like hangars/fighters.
Initialy I am thinking of 4 catagorys:
Tactical pods: These would include pods that, Provide bonus stats to tactical system, provide an additional weapon to be determined by the pod type (more on that later), or provide a clickable power.
Engineering pods: The include pods that, Provide bonus stats to engineering systems, Provide additional engine stats, or again a clickable power.
Science pod: Includes pods that, Provide bonuses to Scientific abilitys, provide additional deflector stats, and yes a clickable power.
Specialty pods: These pods provide less defineable abilitys like, A hangar bay (pre equiped with pets), or an auxilary craft (like the aquarius or saucer sep), perhaps auxilary generators.
Tactical pods might be an extra weapon of any currently available type (maybe not cannons) or some special weapons like a beam cannon (think mini lance as this would be a click power) it could house additional targeting sensors and power generators giving you flat bonuses to weapon damage or accuracy (function basicaly like a console)
Engineering pods Might be liek an auxilliard impulse engine imporving your speed and turn rate, or improve stats like warp core potential or efficiency. perhaps house an advanced damage controll equipment (click power).
Science pods might be an auxiliary deflector (with the same type of stat boosts) or a specialised set of research labs (drasticaly improving a single stat) or an increase in sensors efficiency (sorta like a temporary sensors analysis)
Specialty pods may be a hangar deck with pre equiped fighters or repair drones (specific to the bod you equip and not like tha actual hangar pets) or an auxiliary craft like the saucer sep, maybe generators that provide large bonuses to specific power systems or all of them at once for a lower bonus.