Keep your files. If they are not on your computer they won't be there to transfer to your computer when you sync. If you have Match they can download directly, but iCloud in not the same as Match.
Furthermore, I don't know the details of iCloud but really read this:
"You never know when you’ll suddenly be in the mood to listen to a favorite song, rewatch a classic movie, or laugh at that hilarious sitcom episode with a friend. With iCloud, you can have iTunes automatically download new music purchases to all your devices the moment you tap Buy. You can also access past music, movie, and TV show purchases from any of your devices — wirelessly and without syncing.1 Learn more about iTunes in the Cloud" - http://www.apple.com/icloud/features/
Note the above only says "purchases". In the iCloud scenario Apple is, of course, assuming you only get your music from the iTunes Store. 🙂 If you transfer a CD to iTunes it isn't in iCloud. Even with purchases, if an artist decides to pull an album or movie from iTunes Store it will no longer be there.
Summary of above: Do not delete the files from your computer and also make sure you have a backup copy because there is no other guarantee you will have access to another copy.
