Do you mean that when you open the system all the way, the hinge snaps into place and makes a soft clicking sound? If so, you have nothing to worry about. All of the Nintendo clamshell handhelds (The GBA SP and all 3 models of DS) have all done that, and it is part of the normal operation of the system. Unless you stand there and just open and close the thing until it breaks, there is little chance that normal operation will damage your system.
If you mean that the system makes a clicking sound at other times when you are opening it, or if the sound is loud enough to be concerning, that may be a sign of a manufacturing defect.