lowering ground water would mean lowering sea level. Not really a solution.

Raising the mudpiles would make a lot of them stick out of the ground, that messes with the progression system.

I know of no way to raise them, but vast majority of them can still be mined, tho you will often be waist-deep in water and it's really annoying, and dangerous as it's not easy to get out of those pits. Add an indestructible tree, very poor visibility, wet debuff and the fact that you can drown in your own little dug pit makes it mildly interesting :)