1). It would be stupid to make sappers and diggers siege showstoppers. The point is to add them as a challenge for the so-called impenetrable fortresses, and to provide Fun, but not to let Fun happen all the time.
2). If they're digging through soil, then the point of "building walls" is also to build underground walls where they'll be stopped. As long as there's soil, you should be building foundations to your upper-level walls or your existing structures. This seems like a reasonable defense.
3). Moreover, I doubt sappers would invest the energy to dig downwards. I don't think they're going to path for that. The issue that I have with enemy diggers is their pathfinding: How will they determine the most direct way into your fort? Right now, multi-z-level pathing is bad enough as it is when there are multiple ways into the next z-level (with stairs) as opposed to the simple outside terrain with ramps. More than likely, we're looking at simple diggers: They go one z-level down, and then forward, adjusting for rock outcroppiryings (because they have to move fast). I have a feeling they won't path their digging to farther than it has to go.
I'm in the frame of mind that a). This should provide a fun option (thereby, being an option-enemy sappers and diggers should be configurable in the Init file), b). Fortress design should always be a consideration (as Aquillion has stated), and that there should be options for characters to build Forts that rely on cleverness rather than brute force, or whatever alternatives there are to brute force. There hasn't been a game in a long damn time where not killing everything is an option that's as equally viable as wholesale slaughter; it's nice to see a change.
[Edit] As an afterthought, digging shouldn't be slowed down for the player. Yeah, there are ways of handling this: Give dwarves a natural boost to digging (or define natural digging modifiers in the RAWs reflecting racial strengths, which may apply to other skills too); slow down the speed of enemy diggers (because the stress they have to work with and the care they have to make); have the tunnels they dig be special types of constructions that can be filled in (also something you can [d]esignate.); whatever. In the end, however, the player shouldn't suffer, but your enemy shouldn't have legions of Legendary miners either to spare on sieges.