From personal experience I'm going to have to say I do think MND effects the resist rate of spells. While leveling BLM I noticed that Shock would greatly reduce my chances of being resisted.
People are forgetting that MDB is a direct damage reduction, not a resist bonus. Therefore the MDB on WHM mobs wouldn't account for the resist rate people notice. Plus I notice a similar resist rate on MNK mobs as well.
XI Wiki

