Most major NMs have some amount of Breath DMG reduction. In some cases A lot. It's the same thing that murdered atonement on nearly everything after VNMs(Voidwalker not voidwatch.)
In any case, I have little doubt that MDT works the same for mobs as players, regarding breath dmg. It'd be a simple test to do.
And being so simple, I went ahead and did it.
99DRG/RDM
Breath gear: Wyrm Armet+2, Lancer's torque, Glassblower's belt
No wyvern exp bonus
Upukirex
Mob:Orcish Protector(PLD)
A PLD can self shell, but doesn't have any MDB like most mages do.
That was a shell III. So if MDT worked on breath dmg for mobs, the dmg should have been reduced by 48/256(18.75%.) But it didn't change at all.
Mob or player. Makes no difference. MDT doesn't work on breath dmg.