The thing is that digital HDD games are usually smaller than disc games, in the cases where the game has a lot of updates, the dumped files or iso has the full game v1.0 , the DLCs and the updates are separated in the emulator's update folder, cluterring your setup. Digital game have all the needed file in one folder without outdated and unused files (like the PS3UPDAT.PUP firmware files). Also, some disc games need to install some files in the PS3's HDD to function properly (Last of Us, Metal Gera Solid 4, Drakengard 3, etc), which ends up having duplicate files.
I'm switching to Iso only on some selected titles.
The definitive solution would be a custom compressed file format that would include the base game, the DLCs, and the updates all in one file. Something like the WUA format for the digital and disc Wii U games.