The problem has been around for 3 years and it only effects Linux systems and this specific game making it pretty unique but you can find post about this issues from 3 years ago, and i doubt the devs will ever fix it for Linux / Steam deck sadly.
Any way new leaf is my most played game on my steam deck and I either had the option of
Running the game with hardware shaders enabled, this would fix the crashes, but when running to certain spots in the map you would get giant frame drops and when digging or loading up a new asset, after I spent a couple of minutes running around the town it would go away in the same spots but restarting the game in any way would cause it to come back, so every time I played it I would deal with these massive lag / frame drops the game would literally freeze for a couple of seconds them resume, I even copied my shaders cache from running the game with my save on windows to my deck it even loaded the shaders, but that made 0 difference, I did every setting in the emulator and more made no difference.
The only setting that fixed it was disabling hardware shaders suddenly the freezing when moving to certain areas of the map were gone, but replacing this is another issue when you dig mainly near a rock the game would freeze and then crash to desktop, with hardware shaders enabled the game would freeze on digging near rocks but then resume, over time it got worse with hardware shaders disabled digging a fossils not near a rock could cause the game to crash or digging anyway, I tried another Rom making a new save in case it was corruption.
So I had to go back to playing with hardware shaders enabled which stopped the crashes but now the freezes were back, it would always resume after freezing for two seconds but damnn was it annoying and made the game feel to much like emulating it, and annoying.
Anyway the other night I tried something in Linux as on my windows Pc with citra and the same rom and save, I never had these issues,
I came up with an idea it took me hours but I fixed it and it now runs flawlessly on my steam deck no freezes or crashes, with hardware shaders disabled I can dig as much as I want and no crashes been running for three days with not a single crash or freeze in site, so I fixed it, even have the game launch in full screen straight from steam with steam overlay in steam deck game mode and retain a stable 60fps.
This Fix is for Steam Deck and Linux these issues do not affect windows versions of Citra
Essentially i first of all downloaded the Windows installer for Citra on my steam deck / Linux used a application called ProtonUp QT to install it, Added Cita QT exe to Steam and ran it with Proton Experimental, I then configured the Emulator you shall need a mouse and keyboard for this on steam Deck, as it will keep throwing up the on screen keyboard, Select the rom Directory and edited the Config for my Customer Steam Deck layout and configured the controls to what the Linux Version of Citra is mapped to with Emu deck.
Make sure Enabled hardware shaders are disabled, As i still got the Mini Freezes with it on even though i was running the windows client, But now with hardware shaders disabled and by running the windows Version of the Emulator on Linux you do not get any crashes when digging in game and i could get the crash to happen every time by digging in the same spot with the Linux Version or just digging in general that is it for Desktop Linux Users, No more crashing for you or Freezes, Though i have a some tip below.
(STEAM DECK ONLY STEP)
Run the game once you have configured Citra, it shall run like Crap through Desktop mode, So you shall need to make sure Single window and desktop mode is checked, Go back to Game mode and run the emulator then select the game it should now run flawlessly
Extra Steps to add a direct launcher for the game to steam.
Install / Load if using Emu Deck Steam Rom Manger, Create a new Citra Profile and Direct the Exe to the windows Version we installed of Citra QT, Exe, Then Direct it to the room for Animal crossing New leaf, and build Library, You will now have a direct game Launcher for Animal Crossing New leaf on steam while using the Windows Version of the program, Just go to properties first and make sure Run in proton Experimental is enabled and that is it you can now run the game natively through game mode on steam deck with steam overlay, Controller configs, Power modes, Plugins, Screenshots ect, You shall need to configure the emulator settings again though as you did above as it treats it as a new version of citra windows, You only need to configure them once though.
Getting the Mic to work
Another Tip the windows Version of Citra on Linux will not show the Steam Deck Microphone so you need to set up the Mic in the Linux Version of Citra as it shows up on there, Then open the Linux Citras QT Config and copy the Line about Audio / Microphone name and paste it in to the windows version of the QT config, You shall need to do this in desktop mode now the MIC shall work in game and detect your voice, I use it for the microphone in new leaf to call Animals Names.
Another tip for steam deck users run the Game with V sync off and audio stretching disabled, This shall give you a far more stable 60fps and remove a lot of the input lag which makes it hard for catching fish, Also make sure you right click the ROM in Citra and click properties make sure all the settings listed above are disabled.
This may fix other games with similar issues with mini freezes or crashing, It is nice being able to play my Favourite game on the go flawlessly now, Does not even feel like emulation.
Also playing new leaf at 3x res at 60fps on the go with good controls is the way to go, I could never get in to the game when I used citra on my Pc felt unnatural for some reason
Would be nice if the Devs fixed it for Linux Citra as a whole though, So you do not have to do all of this.