Lets keep things constructive and non-hostile. Plantissue, you have a PM.
I believe there is already some logic that makes tankers/freighters, or at least hybrids, spawn in fleets, but I agree that its strange that enemy fleets in deep space have very few or no logistics ships, so I think it could be tweaked.
I like the idea of under-logistics enemy fleets having a CR penalty, but I'm not sure if it would work out in practice, as currently we have no way of attacking logistics elements of fleets without going through the combat ships first. So in practice we'd only see the penalty to CR if we'd already smashed an AI fleet badly enough that we could attack its logistics. If there was a way of 'raiding' enemies and getting to the back lines though, this would be cool!