yeah underground lakes exposed seems to happen somewhat often. i just tried teaching my cousin dwarf fort, and found a site with damned near everything on it, and the magma vent and underground pool were both exposed and right near each other, and the wagon spawned directly between them. surprisingly the dwarfs survived although most of the stuff on the wagon is forbidden and innacessible as the cave crocodiles and lizardmen are wandering around it.
i thought i was picking a safe place for him as the surroundings were "serene". if he doesnt delete the game out of frustration once the fire imps and magma men come out and set the world on fire fighting with the cave pool critters ill have to get the seed off him, that was an awesome site.
also, i use paved roads to stop the cave growths. they seem to give dwares happy thoughts, they use less building materials, and as long as you have plenty of architects around you can make them really fast. especially good for big underground water resovoirs you dont want getting full of tower caps. blocked water pipes are incredibly annoying, the saplings can aparently pop up in any underground water 6/7 or below, and once there they grow happily into fully grown trees even if the water goes right back up to 7/7 and stays that way forever after. ive been avoiding underground water because of this for a while now. i dont think the surface trees are even that tenacious.