Interesting tidbit: both Elysium and Lucrezia have been taking a DRG-NIN melee DPS combination for Alexander Savage. There were no MNKs in either's A3S clear, but there were NINs.

The fact of the matter is that DRG and NIN bring more unique utility to a progression static than MNK does. A NIN is irreplaceable in the same manner that a WAR is: Trick Attack and Storm's Path are simply too good to not take. DRGs are taken mainly for Battle Litany. Raiding right now is all about pushing phases with DPS. MNK's Int Debuff utility is now shared with DRK which parses higher damage numbers than PLD, so raid teams take WAR-DRK. The MNK is then redundant, so DRG-NIN becomes optimal for the aforementioned skills. Then it's just a matter of whether to take BRD-BLM or MCH-SMN.

NINs may or may not be behind MNKs in terms of overall DPS output as an individual, but Trick Attack alone is worth taking a NIN over a MNK for phases where you need as much damage as you can get.