If you install a fresh install of Windows on a new hard drive. Yes, you will have to reinstall all your software.
As for your files. No, you don't have to place them on the new hard drive. You can have them on any hard drive you wish. All you need to do for your files is know where they are located. You can make any shortcuts you wish.
To access any files on your old boot drive. You will have to take ownership and fix permissions. As the new install will not recognize you as having authority to view them. As for accessing files from the backup drive. That all depends on how your backup program works.
https://winaero.com/blog/how-to-take-ownership-and-get-full-access-to-files-and-folders-in-windows-10/
If you are replacing your boot...