I find there is really no reason to use Dark Pulse on Greninja seeing that in provides no notable coverage at all for Greninja. Water/Grass/Ice/Fire is the best coverage available. The only things Greninja hits for SE damage are ghost and psychic types, most of which are covered by its standard moves. Out of the previous OUs, Celebi and Lati@s are hit harder by Ice Beam, Jellicent is hit harder by Grass Knot while Starmie is hit similarly hard by Grass Knot. Gardevoir, a previous NU psychic that is likely to see some usage in OU, is actually hit harder by Hydro Pump. Other ones including Alakazam, Espeon, Gengar, Jirachi, Metagross and Reuinclus.
252 SpA Life Orb (custom) Hydro Pump vs. 4 HP / 0 SpD Alakazam: 227-269 (90.07 - 106.74%) -- 37.5% chance to OHKO
252 SpA Life Orb (custom) Hydro Pump vs. 4 HP / 0 SpD Espeon: 208-246 (76.47 - 90.44%) -- 25% chance to OHKO after Stealth Rock
252 SpA Life Orb (custom) Hydro Pump vs. 4 HP / 0 SpD Gengar: 253-298 (96.56 - 113.74%) -- guaranteed OHKO after Stealth Rock
252 SpA Life Orb (custom) Hydro Pump vs. 4 HP / 0 SpD Mega Gengar: 208-246 (79.38 - 93.89%) -- 43.75% chance to OHKO after Stealth Rock
The three frail ghost/psychics all have a chance to be OHKOed by Hydro Pump after just rocks, Dark Pulse is not needed in these cases.
252 SpA Life Orb (custom) Hydro Pump vs. 252 HP / 236+ SpD Jirachi: 144-172 (35.64 - 42.57%) -- 91.55% chance to 3HKO
252 SpA Life Orb (custom) Hydro Pump vs. 252 HP / 0 SpD Jirachi: 199-235 (49.25 - 58.16%) -- 64.45% chance to 2HKO
252 SpA Life Orb (custom) Hydro Pump vs. 0 HP / 4 SpD Jirachi: 199-234 (58.35 - 68.62%) -- guaranteed 2HKO
252 SpA Life Orb (custom) Hydro Pump vs. 252 HP / 160 SpD Metagross: 185-218 (50.82 - 59.89%) -- 84.77% chance to 2HKO
252 SpA Life Orb (custom) Hydro Pump vs. 4 HP / 0 SpD Metagross: 218-257 (72.18 - 85.09%) -- guaranteed 2HKO
252 SpA Life Orb (custom) Hydro Pump vs. 252 HP / 4 SpD Reuniclus: 227-269 (53.53 - 63.44%) -- guaranteed 2HKO
Out of the three 'bulkier psychics', only SpDef Jirachi can survive 2 consecutive Hydro Pumps. SubCM Rachi and Tank Metagross has only a slim chance to avoid the 2HKO. Still, Dark Pulse hits not enough to make significant difference.
252 SpA Life Orb (custom) Dark Pulse vs. 252 HP / 236+ SpD Jirachi: 213-252 (52.72 - 62.37%) -- 98.44% chance to 2HKO
SpDef Jirachi actually has a decent chance to survive two Dark Pulses if running protect and can either wish stall or switch out to something taking its hits better thanks to reduced coverage when using Dark Pulse. Dark Pulse usually does not worth the moveslot on Greninja.
When talking about new ghost/psychics, Delphox and Malamar are hit harder by H-pump while Ice Beam hits Gourgeist and Trevenant harder. Dark Pulse only hits Aegislash and Meowstic harder. I really don't expect Meowstic receiving much usage in OU as well as being unable to take Hydro Pump too well. Aegislash is a significant threat but isn't taking Hydro Pumps too well unless running specially defensive sets.
252 SpA Life Orb (custom) Hydro Pump vs. 252 HP / 0 SpD (custom): 140-165 (43.2 - 50.92%) -- 62.11% chance to 2HKO after Stealth Rock
Other stuffs Dark Pulse hit harder includes Rotom-W and Sap Sipper Azumarill lol. Dark Pulse provides no notable benefit to Greninja's offensive coverage. It should not be used unless your team is super super weak to Aegislash and friends and is usually an inferior option for Greninja.
You seem to have forgotten that Greninja gets STAB on Dark Pulse and that Jirachi is now his super effectively by Dark Pulse.
252 SpA Life Orb (custom) Dark Pulse vs. 4 HP / 0 SpD Alakazam: 330-393 (130.95 - 155.95%) -- guaranteed OHKO
252 SpA Life Orb (custom) Dark Pulse vs. 4 HP / 0 SpD Espeon: 304-359 (111.76 - 131.98%) -- guaranteed OHKO
252 SpA Life Orb (custom) Dark Pulse vs. 4 HP / 0 SpD Gengar: 369-437 (140.83 - 166.79%) -- guaranteed OHKO
252 SpA Life Orb (custom) Dark Pulse vs. 4 HP / 0 SpD Mega Gengar: 304-359 (116.03 - 137.02%) -- guaranteed OHKO
As you can see, Dark Pulse OHKOs all these Pokemon 100% of the time, without hazards.
On to the rest of the calcs.
252 SpA Life Orb (custom) Dark Pulse vs. 252 HP / 236+ SpD Jirachi: 213-252 (52.72 - 62.37%) -- 98.44% chance to 2HKO (I'd say having an extremely high chance to 2HKO WITHOUT HAZARDS, nice fudging of the data on your part, makes up for the supposed "reduced" coverage as well forcing Jirachi immediately on the defensive instead of letting it paralyze and KO you instead of beating it)
252 SpA Life Orb (custom) Dark Pulse vs. 252 HP / 0 SpD Jirachi: 289-343 (71.53 - 84.9%) -- guaranteed 2HKO
252 SpA Life Orb (custom) Dark Pulse vs. 0 HP / 4 SpD Jirachi: 289-343 (84.75 - 100.58%) -- 6.25% chance to OHKO
252 SpA Life Orb (custom) Dark Pulse vs. 252 HP / 160 SpD Metagross: 268-320 (73.62 - 87.91%) -- guaranteed 2HKO
252 SpA Life Orb (custom) Dark Pulse vs. 4 HP / 0 SpD Metagross: 315-374 (104.3 - 123.84%) -- guaranteed OHKO
252 SpA Life Orb (custom) Dark Pulse vs. 252 HP / 4 SpD Reuniclus: 330-393 (77.83 - 92.68%) -- guaranteed 2HKO
Let's review: Hydro Pump has quite a bit of merit as Greninja's strongest neutral move. But to discount Dark Pulse is silly. To disguise the numbers like you did (not even listing Dark Pulse calcs, using hazards with some calcs but not others and not talk about what differences it makes) is disingenuous and sneaky at best. Explore all the options, thoroughly, before you jump to such a bold conclusion.