No, no reason, it's just easier to type applications than it is to type program files
The path doesn't matter though, you can put them in whatever folder you want to.
Yes, they can be.
First, (assuming win 7 here) navigate to C:\Users\(you)\ and copy whatever folders you want stored on the other drive to the folder of your choice on the other drive.
Then right click on the "documents" link under the start menu and choose properties.
Add a new library, with the path that you just copied the files to, and set it as the default.
You can delete the folders in C:\Users\(you) now.