I own and use the Sony 30, Zeiss 50 and Sony 90, currently with my A6400.
I shop tested the Sony 50 when I first bought into Sony APS C (after many many years with Nikon) with an A6500. I found it too slow in the shop and don't like the fact that it extends.
My assessment of the others:
Sony 30 is fine as general purpose lens, but working distance is a bit short for the smaller cryptic fish which I like to shoot. Depends on the species of course, and your skill as a photographer. I started off using it a lot as a 'go to' lens when you don't know what you will see on a dive, but rarely use it now. My goto lens these days is the Sony / Zeiss 24 with 36125 dome. I never 'bonded' with this lens, but still can't explain why not!
Sony 90 works quite well with A6400 but narrow FOV makes following small moving targets quite difficult. Again, depends on your skill and persistence. Also much better in clear water given the longer working distance. Can get very satisfying close ups of larger fish in clear water. If you are into land macro photography, 90 is a great choice with A6400 and an appropriate flash.
Zeiss Touit 50. By far my favourite lens. With A6500 was slow to focus, but when it did, results were excellent. I moved to A6400 which has much faster and stickier AF than A6500. The A6400 gave this lens' focusing ability a serious 'kick in the bum', making it very usable for most subjects you would chase with a 50mm lens.
Working distance is fine for subjects down to say 30-40mm, bearing in mind you will want some background to give context to a photo. The (expensive) move of camera and housing was worth it for me. The Zeiss 50 focuses significantly faster that the Sony 90, and the focus is stickier.
A couple of points to note for best results: 1) I assume you will mostly use AFC, Tracking and (say) Medium spot for underwater. If not, I suggest you read up on the topic.
2) I also assume that you will buy the Zeiss 50 used, as new price is prohibitive for most. In this case, you need to check that the lens has the latest firmware installed, or be prepared to send it to Zeiss for the free upgrade. With the original firmware, the lens prevents the camera flash from firing for a couple of seconds when you press the shutter, rendering it unusable underwater! Google the topic / go to the Zeiss website. Be prepared to be without the lens for a few weeks while they upgrade it, if you need to get this job done.
Recent update: I have ordered a Sony A7CR which is FF, after agonising between that and an A6700. However, I intend to use it as a 'hybrid' camera with some of my APS-C lenses, and in particular the Zeiss 50 (because I like it so much, and frankly, there is no alternative (for E mount) in FF (or APS-C for that matter). And I will be able to enjoy the opportunities that FF lenses offer... such as they are! (Not much if anything for underwater macro).
Second, when evaluating an A7CII in the shop (no A7CR available at the time) with my Sony 90, I found that I could not detect a difference in AF performance with the 90 on my A6400 vs the A7CII.
Could be my test (which comprised seeing how sticky the AF rectangle was in dim parts of the shop) but I reckon the lens motors are the limiting factor on the better Sony bodies, at least with macro lenses.