In what directory are the saved games stored

Here is what happens when a pirate bounty is set:

1. A pirate fleet jumps/appears into the pirate system.
2. They select one of the closer planets (not guarenteed though) of the target race that has the bounty.
3. Their fleet then heads for that sector.

If you or your ships are along their flight path, they'll exchange potshots as they fly past each other. However, if your ships are outside of their flight path, they'll be completely ignored even if they're in the same sector.

Once the fleet reaches the sector, they'll start destroying anything in that sector and their various ships will prioritize depending on their functionality (i.e. pillagers will start the bombardment right away over everything else). At this point, if your ships just happen to be in the sector, they may become targeted by pirates.

As for pirate structures, the only pirate structures that exist are in pirate bases, and they are hostile to everything. Expect to be targeted immediately when you jump into a pirate base.

My preferred method of holding a star is to use a Starbase and a few capital ships, along with two or three repair yards. This is also an excellent way to train up capital ships preparatory to sending them out on assault missions.