Not sure if I understand your question correctly but Aroma comes with the FTPiiU plugin. With this you're able to access all storages with FTP, including the "romfs" (/vol/content) of the currently running title.
Or are you talking about .app files? If so they get decrypted while installing them to the Wii U because the NAND and the USB drive of the Wii U are encrypted already. This is different to the 3DS which IIRC uses .app files as copy protection for installed titles as the SD card is formatted with FAT32, so no filesystem level encryption.
So again you're able to access the decrypted content with FTPiiU. An alternative would be to decrypt the .app files on the PC (CDecrypt).