You're right, the ninjas are even more annoying to hit in SoRR than in SoR3. I guess I just remembered them being worse as they're one of the most annoying enemies in that game, but I definitely think you're right about their hitbox always not being exposed when they land from a jump.
My issue with double vaults being pretty much guaranteed to work is not so much that bosses should never be open to cheap tactics - it's that you should make the player work out what tactic works best. I mean, yeah, SoR3 had a lot of enemies you could simply jump kick repeatedly, but SoR2 had much better variety I thought in terms of what enemies were vulnerable to.
"Pause Delay" just sets the characters punch combos to be either SoR2 speed (slower, more technical), SoR3 speed (everyone attacks fast), Remake (a sort of middle ground between SoR2 and SoR3) or Combined which sets all characters to fight like they originally did in the games they're from (SoR3 characters can punch quickly, SoR2 characters punch more slowly with longer hitstun). I personally like Combined, balances out the extra damage that the SoR2 characters do.
Anyways, the issue with double vaults is for most enemies you can regrab without needing to stagger the enemy with a punch in between grabs, making pause delay irrelevant. I am exaggerating a bit with how much double vault regrabs are broken though, as it seems different characters land a different distance away from the enemy after a double vault. For instance, Roo lands almost right next to the enemy whereas Elle has trouble regrabbing certain enemies before they move away when double vaulting.