Why shouldn't you count cargo boxes ? It's more mass so it'd take more damage to destroy, even if it's only by virtue of having a large amount of "padding".
You should count cargo boxes.... along with every other box, treating them all
equally.
All of the boxes absorb damage. One box = one Federation Commander/SFB "damage point", if you like. If you only count hull/cargo, then the proportions are out of whack and you get ridiculous results that just don't agree with the "SFU database" that all the games are built on. Example: Small freighter, has 25-30 combined hull and cargo. But pretty much nothing else. Total boxes of all types ~40. A good blast from a frigate will blow it up. Heavy cruiser: far fewer hull boxes, 10-15 depending on faction, but many more other boxes (warp engines, weapons in particular). Total boxes ~100. A good blast from a frigate will maybe get close to 50% damage, if the shield is already down.
Same thing with the SAL (presume that's the 150-pt ship you mean), it's fairly big so it gets similar damage points to a cruiser. Does seem a bit under pointed, although it does have more limited firing arcs than most cruiser types (except if loaded up with drones, and they can be evaded or shot down).
The SAL is light cruiser-sized. Around 80 boxes/ FC damage points. That, plus stealth, should make it almost as hard to kill as a CA.
I think the error in translation is the differing way that ACTA and the other SFU games handle the degradation in capabilities as ships take damage. ACTA treats "damage to the structure of the ship" and "reduction in capabilities" separately, as damage points and critical hits, respectively. The SFU combines the two. If (for example) your warp engines suffer some damage, that not only reduces the amount of power you generate it also brings your ship closer to destruction.
I'm sure that many NA players don't see the problem. "So what if there are inconsistencies? This is ACTA, not SFB or FC, right? You can't make ACTA into SFB!" The
results in each game must be consistent, for licensing reasons (I believe) and probably other reasons. The
results must be comparable, even if the method that you use to get there is radically different. So when a frigate unloads an alpha strike into a freighter, that freighter should be dead. An Orion Salvage Cruiser should fight an enemy light cruiser on roughly even terms. And so on.