If you already have encrypted files (like those dumped directly from a physical cartridge), you can decrypt them yourself using specialized tools:
This is currently the "gold standard" for safe, high-quality ROMs. Look for "Decrypted 3DS Fullset" uploads. Because it is a library/archive, the download speeds can be slower, but the files are generally free of malware. where to find decrypted 3ds roms
Modern versions of Citra can sometimes handle decryption if you provide the system's shared font and AES keys from a real console. If you already have encrypted files (like those