Have you ever been in line for the ride and had to wait a little while between one train leaving the loading area and the next arriving? I have, so I assume this happens normally. Running 5 trains ensures that there is always a train ready to load, and therefore increases capacity.
Well.... Not necessarily. Though I haven't ridden Everest yet (2 more months!), I've gotten a decent feel for the operations from a few videos I've seen online. (And used my knowledge of how coaster systems work in general).
The key factor in running the attraction at maximum capacity isn't necessarily less just because riders at the load platform have to wait for a train to come in from unload. But rather it's whether the train is loaded and locked and then has to wait for a clear signal in order to dispatch.
If the CMs can get a train loaded with passengers, locked, and they're still waiting for the computer to give a clear signal to dispatch, then they're running the attraction at the highest possible capacity. The more consistently they can get the trains loaded and ready before the first possible moment for dispatch, the higher the hourly capacity regardless of whether or not an empty train was available right away. But if the train is loaded and the earliest-posisble-dispatch point has passed, then the capacity is lowered. I believe that if you (consistently) see a train near the top of the main lift hill as another train is exiting out the front of the mountain, the ride is running at maximum capacity.
I'll use my favorite coaster (Superman Ride of Steel here at Six Flags new England) as a simpler example. Its maximum capacity is two trains. Let's say that Train 1 has just been dispatched onto the track, and Train 2 is pulling back into the station to be unloaded and then loaded. No matter how fast they load Train 2, the computer won't allow it to be dispatched until Train 1 has reached a specific point on the track near the end of the ride.
So if the employees can get Train 2 loaded quickly, and are then standing there waiting to push the Dispatch button the moment the computer gives the all-clear, they're running it at the maximum throughput for that coaster.
But if unloading and loading are slow, Train 1 will finish the ride and come in and stop on the brake run. It will then sit there and wait until Train 2 has finally left the station. (the term for this is "stacking" the trains, and it happens more often than not on Superman) Every minute that Train 1 sits on the brake run is wasted time, and detracts from the hourly capacity.
-Rob