While this is an uncommon issue, some developers do restrict their apps from being downloaded to devices which don’t have the GPS feature, not taking into consideration the fact that an external GPS will allow their app to work. We suggest that you either ask the app developer to remove the restriction or choose a different app.
The vast majority of app developers do not put these restrictions in place, and there is a very large number of GPS-enabled apps which can be downloaded to non-3G/WiFi-only iPad devices, allowing them to be used for navigation (car, boat, plane), hiking, golfing, geocaching, etc.