Attraction capacity = how many people per hour can experience it. The method they used to enter is irrelevant.
Theoretical hourly capacity = how many people could theoretically experience the attraction in a perfect situation where the max number of vehicles are online, every single seat is filled, and there are absolutely no delays, not even seconds of delay. This is close to impossible to achieve the majority of the time, so parks define...
Operational hourly capacity = as a realistic expectation of how many guests can experience the attraction per hour.
Fastpass/Lightning Lane/Express/Virtual Queue etc. do not affect capacity, they affect ridership. Ridership is how many people are actually riding the attraction, how many people are in the queue, how in demand it is based on other park factors, etc. For example, Fast & Furious Supercharged has a very high capacity, but typically low ridership. However, it's ridership increases the busier the park is as more and more guests are looking for anything to do with a shorter line.