No one would miss them, just do it, PLEASE!
Why bother with the mother ships? They’re just captured vessels belonging to someone else. Whe know where the pirates live. You can even look at satelite photos of their villages (both of them). There are over a thousand pirates, just take out the villages. It’s not like anyone would object except for the pirates.
This is one of those cases where “they needed killing” is a justifiable reason for wiping them out.