I decided to look into how your router tells your device where it is, and found this:
iPod Touch: How to Change Current Location
which led me to the Skyhook service, which is cool and slightly creepy:
Skyhook: How It Works > Coverage
So it appears that actually Skyhook is built into your mobile device, and asks their service where the router you are using is. So if your router is mobile that is a problem.
What I haven't found yet is "how does Skyhook know where my router is" if I never told them with their web form? Could be my 3G iPad told them, and so my iPod touch is benefitting from that afterwards.
No - your router broadcasts a unique identifier that anyone can detect, including your iPad. Skyhook goes around in vehicles and looks for these signals, then triangulates their location and stores the location and the router's identifier in their database. So then your WiFi iPad talks to Skyhook and says "hey, I'm using the router with such and such identifier" and SkyHook looks up that identifier in their database and says "Ah Ha! I know where you are! You're at lattitude X and longitude Y"
If you move your router, Skyhook won't know about it, at least at first. So if you relocated to Washington D.C. from Dallas, and brought your router with you, at least for a while your iPad would think its back in Texas. You'd either have to wait for SkyHook's vehicles to pass through your area again, or you'd have to go to the link you posted above to correct your router's location in their database.
So that's the issue with a mobile router and Skyhook - I guess if you know your location when you're out and about and update it in their database using that procedure, it would work, but its manual and a pain in the butt. Also, if you were really on the go, like a passenger in a car, your location is changing all the time so updating it manually through Skyhook wouldn't be all that useful.
So I guess at the end of the day I sort of answered my own question - bottom line is location services on the 3G iPad probably works much better and much more seamlessly than a WiFi iPad using a mobile router from one of the cell phone companies.