For me, the FAQ entry on temporary vs permanent ability bonuses barely provides clarity on that specific question and provides zero clarity on the question of how ability-damage penalizes a character.
What we do know is that temporary bonuses to an ability score do not increase the number of times an action linked to that ability score can be used: i.e. bear's endurance doesn't let you rage more often, eagle's splendor doesn't let you lay on hands more often, fox's cunning doesn't grant you more spell slots, and cat's grace shouldn't boost the number of times per round you can make an AoO. Just so, ability damage shouldn't affect how frequently these types of powers can be used. Ability damage affects "skill and statistics" and provides examples. How frequently a power can be used doesn't seem to be considered a "statistic" in the same way that one's attack bonus or armor class is.
So, I don't believe that ability damage should reduce a Combat-Reflexes character's AoO's per turn as the that number is based on their dexterity bonus, a value which dexterity damage does not change. For me, the numbers of AoOs per round and the numbers of Lay on Hands per day both fall in the category of frequency-of-use, i.e. "other bonuses." The rules on drain really highlight the differentiation between ability drain and ability damage.
"Ability Drain: Ability drain actually reduces the relevant ability score. Modify all skills and statistics related to that ability. This might cause you to lose skill points, hit points, and other bonuses." The bold is mine. This tells us that dexterity damage does not actually reduce one's dexterity score. The penalty it applies is not to the score, nor to the bonus, but rather just to related stats.
Ability drain, unlike ability damage, would actually change ability bonuses. It calls out the things other than "skills and statistics" which could be affected, including skill points and "other bonuses." Abilities which can be used a number of times per period (lay on hands, channel energy, spell slots, AoOs w/ CR) based on some ability bonus would be affected.
Caveats: I'm RAI agnostic and don't believe there is such thing as common sense when it comes to adjudicating the rules of a world of wraiths and rapiers.