Downloading from the PSN serves two purposes:
1.) You get a truly untouched version of the game if you just use the EBOOT. Some .ISOs are modified/condensed/compressed by uploaders, and a lot of older .ISOs were dumped before an issue was fixed with the CFW USB connection, therefore, they are missing bytes at the end of the .ISO and are not perfect dumps.
2.) A lot of games have received updates since release. In a lot of cases, rather than having a download for the game and a download for the update, the updated version of the game is uploaded to PSN. This changes the download size, but also removes the need to download the game and the update separately. Not all games are like this, however. Last I checked, Disgaea 2 is a standalone updated EBOOT, while Elminage Original requires you to download the game and an update separately.
Vice City Stories is an example of a game that received an update at some point, and I believe the PSN link is the updated version and does not require a separate patch.