Shortcut for Applications Folder INSIDE my main Applications folder

No idea how it happened, you may have hit the Cmd-L keystroke to make an alias, may accidentally have dragged the folder while holding Cmd-Alt; some "drag installers" have an alias for the Applications folder which you might have dragged in along with the app; or it might just be a bug in some software installer.

It's ok to delete it, it shouldn't be there.

 

There's nothing wrong with putting items IN the trash. Snow Leopard finally has a feature to restore items in the trash to their original location, so if you have a previous system make sure you remember where the item was.

Obviously, as long as you don't empthy the trash, the item can always be returned.

In this case, it doesn't matter, but for future reference you can can move an item, and if something stops working, then you know you can return it.