Fun notes about boat rides:
The spacing between boats is called the "dispatch interval" and is carefully timed, sending boats as frequently as possible while still allowing spiels/effects to reset and fully play.
Yes, the dispatch interval does change with how many boats are on the flume. The ride's computer keeps track of how many boats are out, and tells the cast members the resulting dispatch interval before they can send the next boat. More boats on the flume, quicker (and closer) dispatch interval.
The boat count DEFINITELY has an impact on capacity. More boats = noticeably less wait time; if some boats break down or have to be taken backstage, you notice that too, unfortunately.
It is considered part of a good ride operation to adjust the boat number as necessary. When wait times die down, it's good form to take boats back to prevent (as mentioned) boat-bumping at the end of the ride, and to minimize the chance of guests seeing another boat's show scene.
Some parks/attractions do this better than others. Many managers prefer not to mess with the boat count because it might involve slowing the ride or taking cast off other jobs. I've witnessed this process at both coasts and Disneyland seems to do this MUCH better. When I saw Disneyland discretely taking boats off the flume at their version of Pirates, it was almost flawless, done very discretely (almost completely in the dark) and with almost no noticeable change to the ride speed. Much better than I could imagine at WDW.
I'm not sure what the difference is at WDW and why problems like those at Small World and Pirates exist. It's disappointing though; regardless of how you feel about wait time, it's very poor show if it can be prevented, in my opinion. The pirates in the jail scene aren't in nearly good enough condition to hold up to several minutes of scrutiny, as they consistently are under these days (again, ride Disneyland's to see what the scene should actually look like).
It could be any number of technical issues, but it's also entirely possible it's just the result of managers seeking to optimize efficiency and capacity (especially in this FP+) era at the expense of show.
Show should trump efficiency.