I can see the files as superuser when I enter 'sudo nautilus' in the root terminal but when I try to copy or move a file it would pop up with 'The file cannot be handled because you do not have permissions to read it'.

Yeah, i2psnark doesn't make it easy for us to solve this in a good way. Try starting nautilus in the following way:

gksu nautilus /var/lib/i2p/i2p-config/i2psnark

I just tried, and that works for me.

If I shut down Tails i am sure my files will be destroyed and I don't think I can make the i2psnark folder persistent either.

You can. In the persistence configuration tool, add /var/lib/i2p as a custom directory. This will also save the i2p netDb etc. which should speed up the i2p bootstrap significantly. At some point we will add a default preset for i2p in the persistence configuration tool.

An alternative solution to this could be to package the Robert I2P torrent client, developed by sponge. As long as the I2P router is running and BOB is started on it, Robert could be run by the logged-in user instead of the I2P user, which would solve the permissions issue. Restricting the connections it makes should not be a problem, as Robert only makes connections to local ports - the BOB port for torrenting, the I2P HTTP proxy port for the SeaWeed browser built into it, and the I2P routerconsole for trackerless torrents (if the Seedless client is installed in the router).