So, IIRC, one point of the logistics rating mechanic was to present the player with a gradual choice: A small but elite fleet (high LR means increased CR) or a big fleet with low CR. An interesting choice.
Are there new incentives to stay small? The sensor mechanic doesn't seem to be one, since while small fleets are less visible, they also have less sensor range.
I'd not like to end up feeling like I'm doing something stupid when I run solo or just with a few escorts.
Two obvious and relatively minor ones are maintenance costs and fuel use for travel.
Sensors *are*, I think, a mechanic that can reward smaller fleets. Say you're trying to sneak into a hostile port to trade (or simply running dark to avoid customs). Your transponder is off, but any patrols flying around have theirs on, which gives them a +1000 to visibility range. Your sensor range doesn't matter as much here - you'll always see them before they see you - but a smaller sensor profile will give you more of an opportunity to sneak in without being seen. For a concrete example, if there's a patrol orbiting a market, a smaller sensor profile could be the difference between being able to come in unseen from the opposite side or not.
Similar stuff applies if you're just sneaking about in a hostile system. Easier to sneak up on someone that has a transponder on, easier to avoid someone stronger.
Finally, as I mentioned in another reply, some abilities (currently: Emergency Burn) have a cost that scales with fleet size, in this case fuel equivalent to traveling one light-year in hyperspace and CR equivalent to a single deployment for every ship in the fleet. A larger fleet is going to have to be extra careful about using this. I think an ideal small fleet would consist of a combat ship or two and a combat freighter (and, perhaps, a small tanker) to extend longevity. (Hmm, that reminds me - now that "civilian grade hulls" are a thing, might make sense to have a combat tanker, as well. One that doesn't suffer from the various sensor strength/profile penalties.)
Are we going to have a point where we are flying civilian fleets like construction rigs, flying in a hound and trying to defend them against fighters or something?
Well, Construction Rigs don't have much of a point now, and you generally move on from Hounds as soon as you can afford something better. I do like the small-scale stuff myself, though, so ultimately I'd like to extend that feeling you get before your war machine "kicks in" and you can afford anything and steamroll everything.