I, too, am very conscious about picking up funky feet and can appreciate the efforts and concerns here. I’ve never had it and want to keep it that way because I know others who have had it and it’s not fun.
With that said, I’m usually most worried about this in showers (hello, gym shower) or in areas that harbor a lot of moisture. Unfortunately, there’s not much you can do by way of the dive deck. It’s wet. All the time. You could argue that you wear boots and Lycra socks but you still have to do the to and from to don and doff. I just tell myself that the salt water and saline environment makes it less ideal of conditions for the funk. At least, that’s what let me sleep at night. I still don flip flops in the shower. I’ve been on 4 liveaboards and haven’t had an issue.
In all honesty, outside of that, assuming it is warm weather, I go barefoot. I agree that it is safer and more stable especially while the boat is rocking and listing. I have a very vivid memory of a fellow passenger picking up their flip flop foot to cross the threshold of a door and their foot cleared but their flop did not. Not a very nice landing.....Ouch.