Yes.
Combat Reflexes functions just as written.
AoO are not part of a character's normal actions, which are why a 6th level fighter still can only make a single attack with his AoO even though he would get 2 with a full-attack action.
A slowed character is still subject to the penalties of being slowed for the duration of the effect, including AoO - takes a –1 penalty on attack rolls, AC, and Reflex saves.