If there really isn't anything, then most of the data you have filled up is failed installs in the Import Directory. These are the files that get either processed when installing or downloading, and if it fails (usually via some error, such as running out of space) These files will stay until you delete them. The best fix for it that I know of is just going into the Directory via FTP and deleting all the files within the MLC Import Directory. (Don't remember the exact file path, so someone else will have to clarify)
Anyways, as a general rule.. Don't install or download with NUSspli to the NAND. The constant, and large writes it performs will cause the NAND to shit out ASTRONOMICALLY quickly. So unless you want a glorified paper-weight as a console? Get an External Drive.
Edit: Also, where did you actually set the download destination for the files? Because if you did it with NAND, then that's probably the issue. So open an FTP Server and go to storage_mlc/install and delete the contents. Then try downloading to SD and installing.
Double Edit: Remembered the import directory -- storage_mlc/usr/import. If there's anything inside of there, then delete it.