1) yes, you can scuttle structures and units by clicking the striped red button at the bottom middle of the screen.  You get a small refund (Vasari has a technology that increases the % of money refunded).

2) no, they're stuck in one star system.  Any star system which does not have an active pirate base cannot be attacked by pirates.

Now be careful with that scuttle button!  (I suggest removing the Shift-S keybind for scuttle.)  If you're not careful you can accidentally end up scuttling a planet (like, gasp, your home terran) or a capital ship without really being aware of it.  Out of the blue you'll receive a message about how, "We have lost one of our capital ships!" or "We have lost one of our colonies!" and you will think to yourself, WTF?  (This is a bigger problem in the online multiplayer game since you can't just revert back to the last autosave.)  I have done both of those things, btw.  Amazingly, in the game where I accidentally scuttled my home terran, my team won.  You'll also feel like a huge moron when it happens to you.