Brandishes and autoguns are the biggest offenders for anyone who's not rich. Disc guns can also can lay a lot of damage down, but they're rare enough that I don't think it matters. Autoguns will let you delete a Trojan as soon as it spawns. Brandishes paired with a vortex bomb can vaporize crowds disc guns would have to chip at. There are two common factors:
1) you're using a charge attack
2) the charge attack is made of lots of tiny attacks
Increasing the charge times sounds like a bad idea. People with good UVs won't care so much, but poorer players will find the weapons less useable. Simply lowering the damage also could go wrong. I've been told that swords benefit more from damage bonuses than other weapons because they're 50% normal damage. For whatever reason, having two damage types does something like apply the damage bonus twice. I speculate that this is because smaller sources of damage benefit more from damage bonuses, which is reflected by the fact that a Troika will see a lower percent increase in damage than a Flourish against neutral enemies. Split damage essentially splits your damage into two smaller sources of damage, hence the larger effect from the bonus. Notably, the Brandish and Autogun charge attacks are made of lots of tiny parts, so if you just reduce the damage of each part without thinking, you hurt unbuilt characters much more than characters with lots of damage bonuses.
What I would do is this: add up the total damage the whole attack outputs, calculate how much the target's defenses reduce the damage, and then divide that damage by the number of bullets in the attack only after doing the defense calculation. If different parts of the attack are a different size, just divide accordingly, like if one of the Brandish's explosions is twice as big as the others just let it count as two bullets. This is all a very brute forced workaround, but it would stop splintered attacks from benefitting from damage bonuses more than single-hit attacks. In the eyes of the enemy defenses, it would make them the same as single-hit attacks.
You're more or less right in your assessment of why split damage and multiple attacks benefit disproportionately from damage bonuses. In most other RPGs, defense is a simple percentage reduction which means it doesn't matter if the original damage source is high or low. In SK, defense will subtract to a point (until half the damage has been subtracted), and after that starts following a curved formula instead. Since it's been a while, a little made up math:
Skolver has 100 defense.
Knight has a sword that does 300 damage.
When attacking, we find that the inflicted damage is (300 - 100) = 200.
Now we apply a MAX damage bonus (24%), getting (372 - 100) = 272 damage.
A 24% damage bonus lead to actual damage increasing 36%.
Knight changes his Sudaruska for an Acheron, which we'll say has 200 normal + 200 shadow.
When attacking, we get (200 normal - 100) + (200 shadow - 100) = 200 damage, same as the Suda, but the real kicker comes when we apply damage bonuses:
(248 normal - 100) + (248 shadow - 100) = 296 damage
A 24% damage bonus lead to actual damage increasing 48%
Put simply, the reason brandishes and autoguns get more out of damage bonuses is because they have higher base damage. They're given this higher damage to overcome flat defense reductions. Your suggestion, if implemented as stated, would buff them more since they would tank fewer instances of defense. At the very least, base damages would have to be reduced.
If you're already going as far as redoing damage numbers on a bunch of weapons, then instead of this whole business of combining damage numbers together in order to run defense formula on them as a unit, you could change the defense formula to become a fixed percentage reduction like in most RPGs out there, which would give consistent result whether it applies to 1000 damage once or 100 damage 10 times.