There are a bunch of problems comparing this to Real Life, and I've asked for more mechanics that force players to risk Logistics vessels for years now.
Let's start off with Real Life vs. Starsector.
1. In Real Life, nobody uses battleships any more. Even cruisers are basically larger frigates with more ordinance and ECM / ECW.
2. In Real Life, battleships are faster on the open seas than frigates (unlike the silly movie / video game tropes), unless the distance is short and the weather's amazing. Yup, faster. Why? Deeper hulls and more sustained power on their engines. A battleship isn't very manueverable, but in a long race, it wins. This wasn't an accident; nations spent the equivalent of billions of today's dollars making them faster and faster, because battleships were strategic weapon systems, not merely tactical; they inspired fear and dread because of how quickly they might show up somewhere you weren't expecting, and could withdraw to the open sea at will. This was even largely true in the age of sail, although for short distances, they were outpaced by rowed boats (yes, they had rowed warships even relatively late, armed with really big bow guns).
3. In Real Life, the only major engagements between large fleets were the result of both sides deciding to converge on a point of strategic value. Otherwise... the ocean is vast, and back before constant realtime satellite observation was a thing, fleets met only when both sides wanted them to meet.
4. In Real Life, battleships were the long-range fighters, protected by frigates from torpedo boats and later on, submarines, and nowadays, long-range missiles launched from boats and aircraft. In WWII, this turned out to be irrelevant, because aircraft could reliably attack battleships anyhow. So by the end of the war, nobody was using battleships for much and carriers had become the center of fleets. Thus it remains to the modern day, with various caveats. One modern attack submarine is far more dangerous than WWII subs were, and tactical nuclear warheads on cruise missiles or long-range anti-ship missiles make the true value of carrier groups against an opponent willing to use them a little dubious.
5. In Real Life, aircraft carriers have more long-range firepower than any battleship could, with strike radii of hundreds of miles. So there really aren't any battleships that can go kill a carrier at all IRL; there is no armor thick enough to stop anti-ship missiles.
So, basically, Real Life is totally not what Starsector is about. Starsector is a fun game about building space fleets and bashing them on other space fleets, with RPG / strategic aspects on top of that. So there are absolutely no "realistic" reasons why we can't have Space Ambushes.
If we need in-fluff excuses, fine:
1. Smaller ships are faster, because this is space and they're moving less mass with their magic space-engines or something.
2. "Ambushes" consist of said faster ships getting in front of your slower fleet and dumping out Space Chaff, or something, throwing all your high-tech systems into disarray (which leads to "give players a Space Chaff ability that they can use themselves", which is actually interesting.
3. Once said Space Chaff's deployed, the enemy can concentrate on the slowest-moving ships in the fleet, the transports, forcing their tugs (if any) to run away.
4. If we need more excuses, please let me know; everything from having ambushes in debris-filled space, near a convenient large asteroid the enemy hid behind, etc., etc., but some of them would be hard to pull off in the SS engine without major changes to the AI (like, it would need to be able to pathfind, which is totally doable but mildly un-fun to write; I'm tempted to port my node-based pathfinder over to try it some time, though, when SS finally goes Beta).
Basically, coming up with fluffy excuses isn't a big deal. Ambushes that force the player to do something different would be fun. Not having the battleships available for a while would be fun. So why isn't this a feature?
Let's see what might go wrong:
1. Players would hate not being able to just use battleships in every fight. Nah. I think most players would appreciate more layers to gameplay.
2. Players would hate having some random stuff happen to battle conditions. Nah. I think that's a lot of the fun of the game, frankly; when it's same ol' same ol', it gets stale.
3. Whiny people would complain about Realism. Go read the first things I said. SS isn't real. It's not a "representation of WWII naval combat" in any but the vaguest sense. And that's good.
4. People would hate losing logistics ships, because they're so weak. Meh. Make them more combat-worthy, then. Not a big deal. It'd feel like Mad Max: Fury Road; your armed-to-the-teeth Space Tanker trying to survive waves of fast-movers while you sweat out rushing in with your destroyer pack to save the day. That sounds like Fun.