Keep in mind that I have no personal experience with any Sony macro lenses except the 90mm, so my info is second-hand at best. That said, I've seen multiple complaints on Wetpixel about both 50mm f/2.8 FE and the APS-C 50mm Sony-Zeiss having serious problems focusing underwater, to the point of being unable to focus at all. Conversely, Phil Rudin's recent review of A6400 described the focus with 50mm FE as fast and accurate, and the A6400 has an updated autofocus engine (shared, I believe, with A9), and the complaints date from A6000/A6300/A6500, so it's possible that the new generation of body has resolved those issues. However, even with the new body solving autofocus problems, the fact remains that working distance at close focus with 50mm is very short - it achieves 1:1 magnification just 20cm from the sensor plane, and almost all of that distance is taken up by the lens and port, leaving little space for lighting, and none at all for supermacro with diopters.
For myself, I bit the bullet and got a second-hand 90mm. Expensive and heavy, but good working distance and great quality. Focusing speed is okay in good light, but holding the camera steady is absolutely critical - a bit of current or surge moving you around and it will not focus at all. For supermacro, I recently got a Weefine WFL05S but haven't had a chance to take it on a dive yet. Basic tests in my kitchen sink produced a working distance of about 2-3cm from front element, which will make lighting challenging, but focus speed and accuracy seem to be fine.