Basically, the problem is that HE needs to be doing a lot of damage to DDs and CVs, but shouldn't be doing much direct damage to BBs and well-armored CAs. I was probably a bit sleepy last night to not notice it, but the easy way to solve that problem is what I outlined above: have armor thickness reduce HE direct damage.
Armor reducing HE damage is already the case, as far as I know. But even BB superstructure isn't armored very good, atleast not compared to belt armour.
I think that may be one of the reasons why HE damage done to DDs is so inconsistent. They're such small targets that you hitting superstructure or side armor is more down to RNG then actually aiming. Also explains why I seem to do way more damage to CVs then DDs when hitting them with HE.
One thing I can't agree on is CA's having to take massive damage from HE, atleast not from any HE below 203mm. American DDs can already melt anything they meet. Even in the Fubuki (tier 8 japanese DD) I can consistently hit a New Orleans for 3-4k damage per salvo, while easily doding all return fire (american guns have such bad shell velocity).
And if a japanese DD, known for having the shittiest gun stats of all the lines, comes out on top against a same tier cruiser, somewhere the balancing went wrong. The only cruisers I'm afraid of in my japanese DDs are Cleveland and Atlanta, since they actually have the reload and amount of shells per salvo to make dodging hard.
Another way to get HE in check would maybe be an approach where Fire doesn't do damage, but instead only lowers compat capability of the ship while burning (longer reloads, less effective AA, less spotting range, decreased concealment, etc. ...)