[Marty Ward]

SJ,
What do you think about restricting Pirate facilities to the point that the number of colonies did not matter. For example, remove the basic shipyard, research, intel, and any other facility that gives the Pirates a benefit you don't want them to have from the pirate trait, like you did with the resource facilities. Then substitute low production value buildings to give them minimal production.
Then colonies become only useful to Pirates for a limited amount of things, resupply, repair etc and it wouldn't matter how many they got.