I imagine not full. But water shouldn't go more than half way up their sides. 2 inches sounds a lot for babies. As you mentioned, some babies aren't the brightest and can't keep their heads up. Either way, its unnecessary stress. And I don't agree with the method. Snakes don't need baths ever. There are better ways to deal with shedding issues.
Shed or not, its not normal behavior for a ball python to soak. I'd check for mites or other issues. Bathing before a shed will strip the essential oils needed to shed. The oils act like a lubricant for the skin to slide off in one or mostly one piece. No oils, the shed won't go well and come off in pieces.
Just my $.02.
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