They will have some in store, but not many, certainly not as many as the American stores had. Apple knows how to play the market. They will want a line; they will want the illusion that you will be able to waltz into an Apple store and pick one up. Remember, after a few weeks of pre-orders the American store delayed the ship date as well.
If you are hoping to turn up at the store to get one, I recommend coming early. There aren't that many Apple stores in Canada and there will likely be people whose pre-orders won't ship until June 7th hoping to get one early and then cancel their pre-order.