Snakes can hold their breath for a long time!How long is "long" to you?
Also, because they are cold blooded, reptiles in general do not need as much oxygen as mammals, and so they don't breathe in as often.
I have seen my ball python dunk his head before, just checking out his water dish. Even stuck his tongue out under there. His head was submerged for about two minutes it seemed; I've never seen him soak, but I think he was just curious.
Have you seen the video of the diving ball python? Search that -- it's adorable, and may put you at ease.
If you are still worried though, I'd just say to put less water in the soaking dish; maybe only have about an inch of water in there at any given time. I would also take your snake out and do a very thorough check for mites and any other abnormalities which could be causing her/him to soak. Otherwise, it may just be a shed thing, as you've suggested.
All the best!
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