We need a dissenting opinion here. I use autofocus when I can - more than I did before when I had a film housing. That's mainly because I shoot the S2, which has a small viewfinder to begin with, and there are no special optics available on the Subal S2 housing to make looking at it through a mask any easier. In my view, this is the biggest shortcoming of the S2 rigs, at least mine. Seacam housings are said to have wonderful viewfinder optics, so this shouldn't be a major issue for you.
The "hunting" problem can be minimised by using a focusing light even in daylight. I use a Hartenberger mini with a wide-angle reflector on top of the housing.
But there are situations where there is no alternative to manual focus. One is shooting in very shallow water and bright sunlight, where you get little ripples of dark and light passing over the subject. It sends the little autofocus brain in the camera into catatonic shock or something.
The other is when the subject is partially obscured at least some of the time by things in front of its plane - commensals in a crionoid, shrimps or whatever in bushy black coral or sea whips. Things that move in the water. The autofocus will try to shift everytime something in foreground comes into the zone. Here, you need to set focus manually and then make fine adjustments with the camera while waiting for an unobscured shot.