I'm pretty sure it's not exploiting a loophole, and Nintendo knows people do it and support it, to some extent. The game does penalize you in some ways if you TT a lot - you can't exploit it to TT back to a time you had good turnip prices when you have turnips yourself, you stop finding fossils eventually, etc. - but it's nowhere near as bad as in other games. Take Pok?mon and Nintendogs, for example, which are both games that have pretty extreme penalties for TT'ing - you can't take part in daily events at all in Pok?mon (Pok?mon massages, gift items, etc.) and Nintendogs (competing in competitions, shops restocking). And that's for any TT'ing at all - even just correcting for the time changes, or if you want to update the time to another timezone. If you do so, you have to wait at least 24h to be able to trigger those events again.
If Nintendo didn't want us to TT at all in ACNL, there would be similar repercussions - no being able to update your dream town, shops not restocking, no new fossils or gyroids after any TT'ing, etc. Heck, if Nintendo didn't want us to TT, they wouldn't allow you to change the in-game clock at all, or they would at least control it (limited number of changes, only up to 24h to allow the time changes and switching timezones).
And, again, and as UglyMonsterFace said, not everyone has time to play daily in the same way people on here can, and they shouldn't miss out just because other people think it's cheating, to some extent. It's not, I'm pretty sure Nintendo knowingly allows it. If you want to play the game without TT'ing, go ahead, it's your choice, but what makes for a better gaming experience for you would make the game unplayable for some others, so it doesn't seem like it'll be removed, anyway.