252 Atk Infernape Mach Punch vs. 0 HP / 0 Def Fluffy Bewear on a critical hit: 102-121 (26.7 - 31.7%) -- guaranteed 4HKO
252 Atk Infernape Mach Punch vs. 0 HP / 0 Def Bewear on a critical hit: 204-242 (53.5 - 63.5%) -- guaranteed 2HKO
As you can see, the Bewear that has Fluffy took less damage from the crit than than the Bewear without Fluffy.
So yes, Fluffy does still apply on critical hits.
Hope this helped.