I did see some pirate bases in the first 3.5 release, but I think it's like the setting differences between "common" and "abundant" - there's a large jump between the two.
Mostly, it's one lonely little pirate ship, just waiting around.
Perhaps the evil empires attract more pirates per the game configs- I normally bounce between good and neutral, so the local conditions aren't poor enough to create enough demand for pirates.
