Does having bought GTA5 from the PS store, and having all the files on the console mean faster loading. Since I have the physical copy, every tit the game, the disk starts rotating, obviously its like a play-cd for PC games, and the game checks if the disk is legitimate, and reads file etc. but doesn't that disk reading mean slower loading for the game ?
Generally yes, the download versions normally end up having shorter load times (and shorter graphic pop-in times) however sometimes due to clever tricks the developers have done, it can actually be slower to use the download version*.
For GTA V I believe the download version is slightly faster loading but nothing that would make you consider changing versions.
* For example Halo 3 on Xbox 360 used to load a certain amount of files onto the HDD for loading while it's pulling from disk. If you were running the game 'installed to disk' it'd be exceptionally slow, as it was trying to pull both sets of data from the HDD.