It was made non-functional by volcanic activity
As James Cameron said in Starlog #125
As some readers may know, scenes were filmed but cut from the final release version of the film which depicted the discovery of the derelict by a mom-and-pop geological survey (i.e.: prospecting) team. As scripted, they were given the general coordinates of its position by the manager of the colony, on orders from Carter Burke. It is not directly stated, but presumed, that Burke could only have gotten that information from Ripley or from the black-box flight recorder aboard the shuttle Narcissus, which accessed the Nostromo's on-board computer. When the Jorden family, including young Newt, reach the coordinates, they discover the derelict ship. Since we and the Nostromo crew last saw it, it has been damaged by volcanic activity, a lava flow having crushed it against a rock outcropping and ripped open its hull. Aside from considerations of visual interest, this serves as a justification for the acoustic beacon being non-operational.
However, in the original script, a crew member may have turned it off
In this script:
On the mechanism, a small bar moves steadily back and forth. Sliding noiselessly in the grooves. Still functioning. Lambert looks down at her direction finder. Automatic recording. Dallas snaps it off.
So Dallas may have turned off the beacon.