In the base game the instructions specifically say you lose points for uncompleted destination tickets. But the Japan instructions say "The game then ends and players calculate their final scores adding points for their Destination Cards and the Bullet Train Bonus described as follows." See the last sentence of the first column on page 3 here. It does not say you lose points. It seems arbitrary to change the rule, but that's what it says. Maybe it's a typo/oversight? Which understanding is correct?
Yes, you do.
Although it is not exactly specified in the Japan rulebook, the beginning of the rulebook does say this:
This rules booklet describes the game play changes specific to the Japan Map and assumes that you are familiar with the rules first introduced in the original Ticket to Ride. This expansion is designed for 2-5 players
So this is only the rulebook for the expansion specifically; any rules given by the base game rulebook still apply normally.
Another thing worth noting is that if you did not lose points for uncompleted routes, then you would never want to return any routes at all. The rule that says "He must keep at least one of them, but he may keep two or all three if he chooses." would make no sense, as you would simply always choose to keep all of them.