X-Com: Terror from the Deep had that whole thing going on, kind of jet-powered submarines that could fly through both land and sea. Of course they had a bit of juryrigged alien technology helping them by that point in the series but still.. Spore will have 100% alien technology so why not?

They also had all sorts of freaky underwater aliens of course.. those amorphous blobs in the diving suits were my favorite. Freaky.

Then again making the AI for such a thing(air/water/land vehicle) so that it behaves rationally would be kind of a pain wouldn't it? I think they're wanting a really simple interface in Spore, so part of the reason for having air vehicles and sea vehicles and land vehicles would be so that you don't need to do anything more complicated than a simple click. Don't have to click any buttons or hot-keys to make a vehicle land, submerge, what-have-you.
Some kind of amphibious vehicles would be good of course, things able to both move on land and cross water, but can't figure out a very compelling reason for an air/land/water vehicle.. or creature for that matter. If you need them to get someplace fast, well, use a flying vehicle. Not a real compelling necessity to land, as far as we know at this point, in order to do anything that a vehicle does. Course I could be wrong. And I would like to see kinda complex things like APCs in the game, don't get me wrong. Seeing the creatures battle it out on foot would really give some variety to things.