It "may" reduce efficiency, but as long as you don't restrict airflow too much, it seems unlikely to damage anything. It's not like restricted airflow puts stress on the AC blower. In fact, less airflow creates more of a vacuum and causes the fan to draw less energy.
The one thing it can do is cause your equipment to run longer (because of the lower efficiency) thus wearing things out quicker. But, most HVAC systems are not nearly as "fine tuned" to the size of your house as many might think. Most traditional HVAC systems basically have 2-3 speed settings for the fan depending on home size. There is a lot of play between those rough settings where a bit more filtration is not going to put it out of recommended ranges.
I have a very high Merv rating filter on mine plus a charcoal filter, but I change it out every 3 months or so.
Compared to the standard, cheap, barely there filters, the run time and energy usage difference is not enough to notice.