From what I have noticed the enemies tend to target stuff like EWACS ships first most of the time.
Not from some magical knowledge of your ships or anything (hell if you gave an NPR one of your ships it probably not know what the hell kind of ship it's supposed to be even with all the tech data.) But it seems they target sensor ships because they often have the most obvious sensor blip. A big active sensor running I think throws off a really big EM blip, which seems to make my EWACS ships become the first thing targeted.
Looking in developer mode once during a precursor "fight" (the precursors were trying to fire missiles in a nebula, I had to delete them to keep the game running.) I noticed that the only ship they saw of my entire fleet of 20 ships was my EWACS's big ass active sensor, and they were firing missiles at that. As far as they knew it was the only ship there.
P.S. And yea, good idea to have at least some small actives on most of your full size ships. I have a sensor ship carrying big thermal em and active sensors with some PD that does most of the sensor work. But my combat ships carry some actives as well, theirs just aren't nearly as strong or as big as my EWACS.
Having one big ship carrying all your sensor stuff may work better next version, where the AI doesn't just focus all their firepower on the first thing they see every 5 seconds and then go down the line swatting whatever is unfortunate enough to be the next target with the entire fleet's combined firepower. Next version they will spread out their fire, which may work out better for big ships with big sensors yelling "kick me" all over the galaxy.