I was told to create a "mods" folder that would allow modded files to load (as I have the disk version of GTA V). Due to the recent update, my mods folder causes the game to crash. I can play with it deleted but I was wondering if I have to create a new one for the new update or something like that?

Yes you will, because the "mods" folder contains files that are update with the new update (hence the folder name "update" inside it).  Each update you will need to redo your mods folder and replace it with the new files.