Out of the box, no. The Nintendo 64 has a region lockout chip which prevents NTSC (Japanese and US) games from running on a PAL (European) machine.
However, through the use of third-party devices, most games should work. I personally own a N64 Passport Plus which I use to play Hey You, Pikachu! on my own N64. It basically works by using a second, local cartridge to authenticate with the lockout mechanism.
I don't have first hand experience of this, but according to that Wikipedia article, some games won't work even with this - presumably, they perform additional hardware detection, so they might be hard to do anything about. It may be possible to somehow bypass these through Action Replay codes; I don't know exactly how these games perform those checks.
You could also buy a Japanese N64 and bring that home. You'll need a power converter to make it run on 230V, and a TV which will accept the input, but you could run any Japanese game that way, and any US game if you remove the plastic tabs.
As an alternative, if you have a European Wii, at least some of the games might be available on the Virtual Console, saving you the trouble of messing with adapters.
I am not sure about memory cards being region locked, but I can tell you that for the most part, saved games are. Each game is given a unique ID and these vary for the same game between release regions and even just editions in some cases. It is this unique ID that the saved games are stamped with that associate them to that game. As far as one region game is consider, those saved files from another region are from a completely unrelated game.
Best Answer
Games are region locked, you will need a code for the region that your 3DS/2DS is from in order to download it. In other words you'll need a Japanese console to play the region locked Japanese games.
It's the same principle for Pokemon event codes in later games.