3DShell should be able to extract some archives.
I would not recommend using it for file transfer to 3DS though: Many files are compressed themselves nowadays. Can't save much data/bandwidth in many cases. Then there is the slow speed of the console itself (CPU, SD access): You would have to extract big archives which takes time itself, after the time for transfer.
My personal recommendation:
Take out SD for large amounts of data and use the PC to write. Fast, reliable, easy. FTP and/or the SMB based internal function is good enough for small files.
Good luck and have fun!