The monorail does run all day; we’ve quite often taken it to go home in the early to mid afternoon before on the 2nd day of a 2-day visit, so it does run all day (or at least did at some point). In terms of how regularly it runs; it just seems to run as often as there are enough people to fill trains, from my experience.
Whether it would be quicker to take it than to drive between the hotel and the waterpark, though, I’m not sure. I imagine that it would probably be quicker to drive between the two, as even if the monorail is quiet, you might sit for a bit waiting for people to get on.
It’s also worth noting that the monorail station is still a little walk from Splash Landings itself (albeit not as far as it is from the other accommodation options), which may be particularly important to consider if your son has any mobility difficulties. Whereas if you drive to Splash Landings, I imagine you could get from your car to Splash Landings in hardly any time at all.