If a boat is whelmed it means that waves are coming right up to the gunwales, the tiptop of the sides of the boat, and some water is sometimes coming into the boat. This is something you can cope with but isn't pleasant. There seems to be little use for this word in a non-jargon or metaphorical sense.
When a boat is overwhelmed, water is just pouring over the sides and into the boat. This is almost certainly going to lead to sinking, capsizing and other horrible things. The word overwhelmed became hugely popular as a metaphor for anything you can't cope with that is sinking you.
Underwhelmed is a backformation and works only metaphorically. Nobody says "the weather is lovely, the sea is calm, the boat is underwhelmed." It started as a jokey comment, much like saying an actress can display the whole range of emotions from A to B, but these days is used with sincerity and no sense of wordplay by people who just see it as a synonym for "disappointed" or "not excited."