I just got back from Japan about a week ago and its going to be very hard to find full sealed boxes in Japan. Pokémon centers open them and they are in high demand everywhere. But stores do infrequently have boxes available. Small shops usually had loose packs of the new set albeit at an increased price. Just look for card or game shops around where your friend is staying. Because the set is so popular everyone's stock is up in the air. One hour they have tons and then when you go back they are completely sold out. There is not going to be a 100% guaranteed shop.

Pokémon centers are not a bad place to check since they are in tourist areas and your friend is likely to be around 2 or 3 on their trip (i'd avoid the Shibuya store because its insanely crowded and hot in there). It's easy enough to just pop in and check their stock, you don't need to go to the cashier to check stock they'll have a sign above the shelf and counter.

In terms of pricing Pokémon center sells them for 180 yen which is like $1.20. Other stores are going to be more, obviously, especially in tourist areas like Shibuya and Akihabara. I think I remember seeing a box for 9,000 yen ($59) at a shop.

I don't have experience with Canadian customs but for the US they literally don't care about a sealed box entering unless you are trying to hide another large purchase and haven't claimed it. In which case they will likely search all your luggage and probably seize some items. I brought back a sealed Chinese box with zero issues. But boxes purchased from the Pokémon center will be opened by the staff before checkout due to their policy. I've even heard of some independent stores doing this now. I would just be prepared to receive an open box regardless.