I don't think we will have any issues. The only apps I've noticed missing from the Canadian iPad store is the iWork Suite and iBooks (which I downloaded from the American Store). All the other apps can be currently found in iTunes by searching for "iPad" which reveals like 3000 available iPad apps.
My iPad currently uses an American ID so I can browse the App store, but once the Canadian App Store is officially launched, I will just change the iTunes account in the iPad Settings.
Honestly, the only long term issue I can see is updates. When it scans for updates some it will want to update from the Canadian store and some from the American store. I will have to let it update one set of apps first, then sign in with the other account to update the others.