We were able to shop in the World Bazaar (Tokyo Disneyland's Main Street) and the exit are of Disney Seas until about 20 to 30 minutes after closing in the normal shops. They tend to close some doors, but some doors are still open and there were plenty of people inside. However, it seems that the cookie shop will be open the longest. Since boxes of cookies are such popular items there, both parks have really large shops with boxes and boxes of cookies (some with really neat designs, I got a really nice tin that now has my breakfast cereal in it). Those seem to be open the longest. And those are crazy busy. You will see CMs restocking the empty shelves from large boxes and the stuff flying off the shelves at even faster speed than it is being restocked! However, I think by about 45 minutes after park closing they are starting to close down all the shops.
I do agree with
@Agent 86 that it might make more sense to shop during the day and use the park time until the very last minute. We were able to hop on Snow White's Adventure even two minutes after park closing! The line was still open and CMs were waving at us to come and get in line. Not sure if that is usual or what the reason was, there were a few Japanese people who followed us, so I don't think it was us stupid non-Japanese people not following the rules. But by the time we got off, the ride was closed.
Bon Voyage and the gift shops at the hotels are good places for some shopping as well. If you are using the After 6 Passport, you could shop before you go into the park. Also, Ikspiari (the mall at the train station) has a
Disney store and they had some really cute stuff! I think Bon Voyage is open after park close, but Ikspiari is not.
And finally, if you are after specific merchandise, you would want to check out the specific shops throughout the park anyway. For example we picked up a little Trader Sam (from the Jungle Cruise) plush in a shop in Adventureland. This was only available in that one location. Same with the very cute Camp Woodchuck merchandise that is only at the cart outside the Camp Woodchuck restaurant.