I doubt that low pipes would have much trouble in water crossings. I've seen hundreds of trucks back into the water to unload boats, and blow bubbles with their exhaust pipes while the boat was unhooked. Doesn't seem to cause a problem.
I can tell you that the scrambler pipes on my CL450 certainly do make the bike feel a bit wide when you stand on the pegs. You don't notice it when you're sitting. The trouble with the hammarhead Jack Pine bike is that it had high pipes on both sides, which would be even worse than the standard scrambler, where both pipes run down one side. It also had the pipes uninsulated, and unshielded. Those pipes running past your legs would get damned hot without heat shields!
I doubt that you would notice a scrambler being top-heavy, though low pipes would, by definition, keep the weight down lower. For my purposes, I like high pipes because they are not as likely to start a fire in tall dry grass. (I live in a desert where fires start easily.)