I agree, make a vast variety of modules, this makes game interesting. Each module should have a % chance drop or can be unlocked at a certain rank.
Break modules into sections:
Damage
Reload
Sailing
Armor
Crew
Boarding
Open world exploration
etc..
Choose how many module ranks you want to have.
ex. Basic - Premium
Basic - has only 1 bonus value
Premium can have 3 with 1 will be negative. (+5 damage +5 reload -5 crew defense.)