Caissons might be removed, or might be left, in the real world. Depends on the project. Making a bridge footing, for instance, you'd sink the caisson, drive out the water with air pressure, get people into the caisson by various means, have them dig out the mud and otherwise get it ready for filling, then fill it with concrete to make a foundation. caisson stays. Other uses or designs would often reclaim the caissons.
In DF, REMOVING an item under water would be quite challenging. I suppose we could wait until magic is added so we can just put water breathing on some dwarves and let them remove the caissons. But until then, I had an idea--- what about a draw bridge that doesn't raise, but lowers instead? Construct it in the level/horizontal position on constructed "scaffolding" frame over your water target, hook it up to a lever via mechanism, and then flip the lever. It then lowers into position, 1 z level per 1 tile length built. This gives you temporary walls that can be removed later (just raise the bridge). It would be handy for traps and water control (A REAL multi-level floodgate), and if any hostiles ever get set to bridge smasher, guaranteed to be "temporary" until you get a properly constructed structure into place. For large projects, you build many such bridges. For small projects, you just need 4 (1 for each side of the coffer dam), and then you can construct pumps to drain your targetted area in the box. This would be VERY doable in DF, as all the major elements are already present. Only 2 differences between them and standard draw bridges--- 1, they can be multilevel, instead of the folding/accordian drawbridges currentlly in the game, and 2, player instructing the game it wants the bridge to fold down, instead of up.