They used to be used for a number of purposes. One is to send a tone through a channel to trace its route to a patch panel, external FX and back. - in other words to check touting or for fauly finding. Another common use was to add a 50Hz tone between takes on a master tape. When the tape was fast wound you would hear a beep at the start/end of a track. Another common use with tape machines was to add 100Hz and 10KHz tones at the start of a master tape to it could be properly aligned for playback on any other tape machine.
Cheers
Ian