I want to post a brainstorm about all the crashes that have been going on. I tried to do some research on my ideas and could not find much (or understand much of what I did find), so this is just speculations.
The first thing that came to mind when reading about it was: memory. I have a New 3DS XL and first played Terraria on its 1.0.2 v. I experienced a few crashes where the system had to restart, but yet to have any crashes since updating to 1.0.3. Granted, I have not "played" much on this version because of a project I have been working on since before the update. Also, have not been to older worlds much. I started to think maybe the SD cards shared some of the RAM and people's cards were full of data and downloads. It doesn't seem this is the case from looking at what hardware specs I could find. However, this got me thinking about cards and how I have a hard copy of the game. Am I wrong that the data being on the game card puts less strain on the system hardware? Which got me thinking about the digital version of the game. Is the game data on the eshop some how flawed causing issues? This got me thinking about areas I currently cannot fathom; being a 3DS coded game, could there be some headers or other programming causing the issue on New 3DS systems, or XL systems? I was reading something about memory appropriation according to specific game codes and something having to do with the GPU running on a lower capacity.
Again, this is just my brainstorm and speculations. I hope this gets some ideas stirring and helps get the crash issues solved. On a final note, you can never save too much. Get that auto-save notification activated, and use it when you see it.
EDIT: I forgot to note that I leave my system on for days, mostly in sleep mode, with the game running. Have even left if running all night while farming Pirate Maps in the ocean.