So, is it just me, or does Krookodile not decimate the Deosharp, and even Deosharp + Aegeslash core that is so popular?
Against Deo-D you can naturally outspeed, hit with STAB Knock Off or simply Taunt so that no hazards can be put out.
Except you don't outspeed it cause Deo-D runs Timid max speed and Krook runs 252/252+ HP/Def, Deo-D can Taunt/Magic Coat or just use Stealth Rock/Spikes before you can hit it and Knock Off only has a small chance to 2HKO Deo-D.
4 Atk Krookodile Knock Off (97.5 BP) vs. 252 HP / 4 Def Deoxys-D: 158-188 (51.9 - 61.8%)
4 Atk Krookodile Knock Off vs. 252 HP / 4 Def Deoxys-D: 108-128 (35.5 - 42.1%)
Against Bisharp even if you switch in with Intimidate and give Bisharp a +1, you're still faster and Sucker Punch still does nominal damage.
+1 252+ Atk Life Orb Bisharp Sucker Punch vs. 252 HP / 204 Def Krookodile: 130-153 (32.9 - 38.8%) -- 8.4% chance to 3HKO after Leftovers recovery
0+ Atk Krookodile Earthquake vs. 32 HP / 0 Def Bisharp: 270-320 (96.7 - 114.6%) -- 81.3% chance to OHKO
That's a guaranteed OHKO with Life Orb recoil if he chooses to
Defensive Krook runs Impish, not Adamant and there's no reason to stay in on Krook at +1, also Krook needs 80 speed EVs with a neutral nature to outspeed 252 Spe Adamant Bisharp and it can't come in on either SD (unless it's running 80 or more Spe investment) or Iron Head.
+1 252+ Atk Life Orb Bisharp Iron Head vs. 252 HP / 252+ Def Krookodile: 226-266 (57.3 - 67.5%)
+3 252+ Atk Life Orb Bisharp Iron Head vs. 252 HP / 252+ Def Krookodile: 376-445 (95.4 - 112.9%)
+1 252+ Atk Life Orb Bisharp Iron Head vs. 252 HP / 176+ Def Krookodile: 243-289 (61.6 - 73.3%)
+1 252+ Atk Life Orb Bisharp Sucker Punch vs. 252 HP / 176+ Def Krookodile: 121-144 (30.7 - 36.5%)
As for Aegeslash, STAB EQ obviously does not fear Kings Shield.
252+ SpA Aegislash-Blade Shadow Ball vs. 252 HP / 0 SpD Krookodile: 107-126 (27.1 - 31.9%) -- 51.6% chance to 4HKO after Leftovers recovery
-1 252 Atk Aegislash-Blade Iron Head vs. 252 HP / 204 Def Krookodile: 93-111 (23.6 - 28.1%) -- possible 5HKO after Leftovers recovery
-1 252 Atk Aegislash-Blade Sacred Sword vs. 252 HP / 204 Def Krookodile: 140-166 (35.5 - 42.1%) -- 89.6% chance to 3HKO after Leftovers recovery
Considering the popularity of this core I'm honestly surprised why defensive Krookodile isn't used more. Fighting, Water and Grass moves (Keldeo aside) and not terribly common in OU compared to other types, and Intimidate users that can Taunt and set Stealth Rock are always welcome on top of STAB Earthquake and Knock Off. Admittedly Ice and Fairy weaknesses are the issue. Thundurus-I is top of the charts currently, but even HP Ice is a gamble.
252 SpA Thundurus Hidden Power Ice vs. 252 HP / 0 SpD Krookodile: 170-202 (43.1 - 51.2%) -- guaranteed 3HKO after Leftovers recovery
You can't tell me that isn't impressive.
Krookodile isn't bad, it certainly has some use in OU as a defensive rock setter that checks/counters some important threats, most importantly Aegislash (counter), (Mega-)Tyranitar (counter) and Bisharp (Check).
I wouldn't advice checking Thundurus with it though, unless you scouted it to not have Focus Blast:
252 SpA Thundurus Focus Blast vs. 252 HP / 0 SpD Krookodile: 340-402 (86.2 - 102%) -- 50% chance to OHKO after Stealth Rock
252 SpA Life Orb Thundurus Focus Blast vs. 252 HP / 0 SpD Krookodile: 442-523 (112.1 - 132.7%) -- guaranteed OHKO
Or even Grass Knot:
252 SpA Thundurus Grass Knot (80 BP) vs. 252 HP / 0 SpD Krookodile: 228-270 (57.8 - 68.5%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
252 SpA Life Orb Thundurus Grass Knot (80 BP) vs. 252 HP / 0 SpD Krookodile: 296-351 (75.1 - 89%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
Let alone the more uncommon physical Thundurus set:
+1 252 Atk Thundurus Superpower vs. 252 HP / 252+ Def Krookodile: 298-352 (75.6 - 89.3%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
+1 252 Atk Life Orb Thundurus Superpower vs. 252 HP / 252+ Def Krookodile: 387-458 (98.2 - 116.2%) -- guaranteed OHKO after Stealth Rock
+1 252 Atk Thundurus U-turn vs. 252 HP / 252+ Def Krookodile: 176-208 (44.6 - 52.7%) -- 22.3% chance to 2HKO after Stealth Rock and Leftovers recovery
+1 252 Atk Life Orb Thundurus U-turn vs. 252 HP / 252+ Def Krookodile: 229-270 (58.1 - 68.5%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
That being said Krookodile is by no means a bad mon against the common HO Deo Sharp Aegi core, but it's not as much of a counter as you made it seem.