Back for some more feedback!
1 - I finally discovered what the "Piles of Junk" that we start with are.. By looking for something completely different in the workshop list, seeing I could use them for something, and then going to look in the bootypedia to find an article I had never seen. I went back in my saves and figured out it was made available when I got "Spring Cleaning", but somehow it doesn't show up with the Decrypted Data Disk in the "We can now manufacture" window. It would be quite useful to get it, or to put a mention in the Spring Cleaning article that we "should get the runts to clean up the rest of the junk" or something, since the pile of junk article itself doesn't pop up either.
2 - The Harpy's Nest got attacked by a boarding torpedo and a very fun battle followed, but I noticed something in your base defenses (and terrors to some extent): The variety in enemy units plays a lot against the AI. In this case, it was traders, and between GOs, Hostesses, Pilots and engineers, I was able to panic the enemy easily with casualties and keep them from being too much of a threat.
It seems like if Traders are fed up with the pirates and send a crew to take them out, they should send more personal/power armor dudes and fewer civilians. The 3 enemies in power armor (and the few in personal armors) caused me pause, but all the fodder was great for keeping the gals' morale high while crippling the enemy, making the base defense fairly easy.