These are common fixes for Mods not Working for Minecraft 3DS.
Multiple Game Instances:
If you have multiple versions of Minecraft from either other regions or a Game-Cart with a digital copy. These will interfere with Mods being loaded.
You should only have one version of the Game on your system at a time.
DLC/Update + Game:
Sometimes if you have a region-free game or DLC/update and a USA/EUR/JPN copy of Minecraft 3DS. They will cause mods to not fully work or at all.
Make sure you have everything matching the same region, and nothing is amiss/mismatched.
LCL:
Make sure Luma Chain Loader (that select thing you probably did once at startup and never again), has "Game Patching" enabled.
Hold Select at Startup to get too this Menu.
If the option doesn't show a [X] on Game Patching, then it's disabled and needs to be enabled.
Download Mods for your Game's Region:
Sometimes we mis-click or it doesn't get registered. The Minecraft 3DS UniStore has an Automatic Installation Process.
Make sure you're installing your Mods to the correct Game, as this could be the Reason.
Combatting Mods:
Some Mods such as Skyblock+ (Plus) and Amplified World Generation combat eachother, and cannot be installed together on the Same system.
Make sure your Mods don't conflict by Sending a Message or Pinging the Creator in the discord server here. We're always happy too help!
Game Version:
Nearly 100% of Mods for Minecraft New Nintendo 3DS Edition where made only on Patch v1.9.19.
Make sure you're fully updated with the correct Region Update/DLC.
Incorrectly Made Mods:
Let's face it, some Mods are extremely buggy or at best "Meh", maybe they broke with time, who knows.
Try installing another Mod, and see if that Works.
Mods not installing:
If your Mods aren't installing from the Minecraft 3DS UniStore, you should try reinstalling the Store itself.
Delete the UniStore from the Settings Page on Universal Updater, and try a QR Code from this Link: https://github.com/Minecraft-3DS-Community/minecraft-3ds-unistore
Still Having Problems?
Share your thoughts in in the discord, we're almost always active and ready to help, just give us some time, and we'll get back to you.