need an excuse to make turtle shell cracking hard? so make a use for adamantium or steel mining equipment. not that you would want to go digging holes in your turtles shell. i dont really see delving into the turtle itself to be something you really want, unless your fort is starving for some reason or perhaps you need to do some medicinal work on your mobile home. dwarven miners doing surgery inside a giant turtle sounds great, but im not sure how it would fit as a gameplay element in DF. i just figured turtles would be more or less invulnerable, implementing its internal organs and an ability to kill it would need a whole slew of difficult to sort out game mechanics.
as for the turtle swimming, with something sufficiently buoyant stuck on its back it would not be able to submerge. real life turtle sometimes get this problem from an excess of growths on their shell, and occasionally from serious blunt trauma injuries that result in gas pocket inside their bodies. not that you need "realism" like that to excuse anything to do with a game about dwarves riding giant turtles.
in the DF engine, i envisioned the turtle being more or less a huge stationary object in the landscape, which could be moved around by entering the world map and choosing a new fortress site. then a path would be found across the world for the turtle to travel, and the likeliehood and type of random encounters of the kind you get in adventure mode sorted out. the turtle with whatever you have built upon its back could then be placed into the landscape on arrival like many of the current map features are. hopefully not several z levels up above a magma vent, like a goblin tower i found once a while back that collapsed as soon as i arrived.
so, in a moving turtle fort, you would likely have sites around the place geared up for spending a season at to farm large quantities of food and mine and smelt a large amount of ore. moving around like this would also mean you could select a town to plonk down outside of to trade, or attack and pillage. your temporary homes around the place would probably have things built specifically to keep your moving chelonian mayhem machine going. dropping in on these sites would be a little like reclaim mode. you could make things things like a large magma aqueduct to dribble some red hot glowing goodness into a stone storage tank somewhere on the turtles back, to be used for item forging or defense. you would probably want to do the same with a small amount of fresh water, to treat injured dwarves. if the turtle could cross oceans, you could find peaceful unassailable islands to farm and train on without risk of ambush or siege.
anyways, as people have said before, this idea is awesome but would be a lot of work to implement, and would probably change DF into a completely different game. imagine trying to locate your abandoned turtle fort in adventure mode when it keeps wandering around the place?