Before the patch, yes, both physical and digital versions of the Japanese version suffered from slowdown, glitches and corrupt save files. Our copies came pre-patched with patch 1.1, however, which largely reduces the chances of these things happening.
Granted, there is chances for corruption to happen on the patched copies, as shown by Sats and others. As long as you are careful with SD card/game cartridge treatment, and do not turn off the system while it's saving, you are most likely in the clear. If you'd like, saving once a day at night and backing up that save is an option for people with the digital version although you'd have to do that every day.
Sats, I'd recommend contacting Nintendo of America/Europe with this information, there may be something they can do about it.