I use1/64. May as well save the camera battery, if that is enough light to fire the strobe. It is the strobe setting that determines the exposure, not the camera setting.
Yes, many people set pop-up flash to minimum setting 1/128 or 1/64, just for external flash synchronization in M mode. It is good for camera battery saving.
But pay attention, that such solution is acceptable only for few models of underwater strobes, not for all. It does not work properly for many well-known strobes on the market.
Good example of this is Z-240 by optics, - yes, in M mode it begins burning at the control signal beginning, but not all people know that Z-240 stops burning after control signal end. If pop-up flash produces very short control flash 1/128 or 1/64, then Z-240 also can produce only small power flashes and impossible to significantly increase power by right dial. For normal work in Manual mode Z-240 requires control signal duration longer than 3.2 ms. This is undocumented feature. According it, we must set 1/1 flash power in camera menu. This is reality. I can say even more, - 1/1 camera flash duration is necessary for Z-240 control, but not enough for getting 100% energy. Because pop-up flash has a small size tube and it's maximum duration is about 1...2 ms (but not 3.2 ms !!). Yes, of course 1...2 ms control signal is enough for getting about 70% of Z-240 max power, but the rest 30% is unavailable.
In common case, only LED triggers can fire Z-240 and other similar underwater strobes for full 100% power. LED triggers produce appropriate long signal duration for underwater strobes (usually 5 ms for small strobes, 25ms for large strobes). This is one of well-known advantages of them.