Even if you could prove that an aftermarket intake w/ filter did as good, or better, when it comes to filtering air (compared w/ stock paper filter), you are still putting something on the car for the purpose of increasing airflow. That means more fuel along with the potential for more power.

In theory that could cause piston rings/seals to wear faster. They don't have to prove beyond a shadow of a doubt, just that it's possible. Otherwise people could turbo their cars and Honda would be stuck with the bill when something let go, they wouldn't be able to stay in business.

Besides, the vast majority of aftermarket filters don't filter as well as a stock paper one when it comes to very small particulates. That's more likely to cause premature wear than a mild increase in flow.


edit: That being said, I've used both a K&N filter and a modified intake on my car. However, the warranty expired years ago. I've since gone back to using the stock filter, in hindsight the K&N was a waste of money.