Recently after a series of battles I went to attack an enemy legion base. My first attack was around 20s, my second, over 200. Apparently I had a Ktrap that I didn't realize. <shrug> same damage across board for previous battles so didn't notice too much.

Would it be possible to get a window on the battle tab when we target enemy ships/bases that shows our own ships effects at the same time?

At the top of the Battle display it tells you your Attack and Defense, so you can see if your attack is not what you would expect.