I don't know, but I do know that they will use the well even if the water below it is saltwater.
To add some more confusion for the desalination issues:
Recently, I was also on a map with saltwater and an aquifer. The aquifer, once channeled into, was apparently holding saltwater.
I dug out a room in the z-level above, constructed floors and walls out of rough rocks, built a pump, channeled a hole into it from above, and I had desalinated water. Awesome, and as one would expect.
Then, however, I had the splendid idea to open this reservoir for the purpose of flooding a prospective towercap farm in the z-level below, in the area not covered by an aquifer. The towercap farm region was too large for the simple hole that I had dug into the aquifer to flood it before it would evaporate.
So, I dug a tunnel from my constructed reservoir, put a channeled tile at its end. This tunnel did not have constructed walls. I wasn't thinking very clearly at the time.
I destroyed one of the constructed walls of the reservoir and flooded the towercap farm for a couple of ingame weeks.
During this, I noticed that the water in the reservoir had turned into saltwater, apparently. A water source zone next to the well didn't show any water tiles anymore, that is.
I ignored it for the time being. Then I destroyed the entire reservoir and the pump and did build a new one with rock blocks; the water didn't touch any natural surfaces.
When it was refilled, the water was apparently still salty.
And this is something I don't understand.