It was made non-functional by volcanic activity
-----------------------------------------------

As James Cameron said in [*Starlog #125*][1]
> 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][2]: 

> 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. 


  [1]: http://io9.gizmodo.com/5898580/read-james-camerons-1987-responses-to-angry-fans-who-hated-aliens
  [2]: http://docplayer.net/1161818-Alien-1979-by-walter-hill-and-david-giler-based-on-screenplay-by-dan-o-bannon-revised-final-june-1978.html