I strongly recommend against most anyone doing this in water. Given what it's, it would seem to leave a hole below the water line with all of the obvious risks.
Having said that, I have done similar in water. And the water can be manageable. Even a 3/4" thru hull near the watering won't sink a boat fast and the flow can be mostly stopped with a hand or foot on the inside or a plug or plunger or wax putty from inside or out.
If I, with due consideration to the risks, decided to remove it in water. I'd replace it with a thru hull if large enough or a 316 stainless bolt, otherwise. If I did it with a bolt or thru hull I didn't want, I'd take it out and do the fiberglass work at the next haul out.
The basic idea would be to have the bolt or thru hull ready. Remove the device with the assistance of a diver and control the water flow with a plunger or otherwise from the inside until ready. Let a diver goop the thru hull or bolt with 5200, pound on the hull with a pipe so I could remove the plunger, and let the diver push it thru and hold it in place while I got it started from the inside. If I needed to make the hole larger, for example for a larger thru hull, I'd use an air drill (, but have also seen it done with battery drills). The diver is done and just on standby once it is started as it can be held from the inside after that point.
If installing a thru hull, I'd fill it with wax plug paste first, so once it is in, it won't leak. Then, after tightening, I'd knock it out with a dowel and cap it off. From there a bolt can be cut off.
If concerned about a round bolt head underwater...remember zincs have thru bolts.
To mitigate risk, one wants a good and experienced diver or two, and a good or experienced helper or two. As much as possible, plan with them, let then do the work, and stay thoughtful, calm, and ready to manage things as needed if something comes up. A trash pump is never a bad idea, etc.
Again, I am reqlly not suggesting that one do this. Just that people make choices and some might choose to do this, including.me under some circumstances. There is obvious risk.