Ignoring, for a moment, any design reasons for the cover, ask yourself the last time something spilled on your desk. In addition, covers do serve a functional purpose. Most computers are designed with air circulation in mind. Removing bezels, and covers affects the intended air circulation causing a potential heat problem. If after doing an install, you find you can't open your CD-ROM, or eject disks, check and make sure that your cover is on properly.
Many covers use bezels with buttons instead of the button actually on the drive.
At this point, most computers will need a device driver installed to use the device. Some machines will register a BIOS error if any change is made, or even if the cover is opened.