Well here's a weird thing. I emailed Pilot's support and they asked for screenshots. I made some of the Clipper and some others with default and 'official' floatplanes for comparison (the Beaver, Ford Trimotor and Hughes Hercules). Then I went back to the Clipper to get another shot from a different angle. It showed convincing spray and wake effects. I tried again after reloading MSFS, and then after a reboot and still the effects were working. I've no idea how or why this happened, but hopefully it stays this way.