There could be so many different ways to go about why, or how. They have plenty of textures, and it would make for an interesting aspect to play upon.
They could be hostile, they could go to war, the possibilities where Bethesda would want to take it are endless because the lore basically says nothing more than they just vanished. They could even make it be as crazy as involving portals and other "plains" but i don't think it is necessary.
They could put together huge, and i mean huge underground cities, far, really far below the surface. They could be friendly, and have there own missions, or they could be alittle bit of both. Perhaps a currupt king, undead king? Undead dwarves?
They could even add the landmass of Morrowind that boarders Skyrim and have a-lot of it take place there, and travel underneath Skyrim.
These are just some ideas.
Thoughts, comments, concerns?