Q: How can I delete apps that are on ICloud but not on my iPhone 5S

Can you please explain what you mean a bit more?

Apps cannot be in iCloud and they do not take up space in your iCloud account. If they are not installed on your device, then there's no place to delete them from.

The only other the option is your Purchase History, All the apps you have ever purchased will  appear there, but they cannot be removed. You can choose to hide the Apps, but since apple uses this list to determine what apps you have purchased so you can download them again without paying you cannot remove them form this list.

Hide and unhide purchases in the iTunes Store - Apple Support