I would highly recommend time traveling by using the in-game clock rather than messing with the system clock. If you play any other games that have daily events like Pokemon then, like Cryptade said, you are unable to do them for 24 hours. I guess that's sort of an anti-cheating measure. Meanwhile, changing the in-game clock in New Leaf has no effect on any other games, so you have nothing to worry about.
I'm a big time traveler but the only time I ever mess with the 3DS clock is to adjust for Daylight Savings Time changes twice a year. If you want to keep track of your last play date and time you can write it down or make a file on your computer that you can update.