Lookong at images of the Pioneer HLD-X0, I notice that it has indicators for Digital Data Off and Clock Ref: Video/Audio. What are these for or what do they do? Are they related only to MUSE LaserDisc playback? Im just curious about them because I've never seen anything like them on other players.

The HLD-X9 has those features as well and there is some discussion in the following thread on the purpose of the clock ref.
viewtopic.php?f=23&t=567&hilit=Clock+Ref

HLD-X9 has the same indicators on the front panel.
(from left to right: D-EXT / DIGITAL DATA OFF / CLOCK REF VIDEO / AUDIO [[ DISPLAY ]] DISPLAY OFF / SIDE A / SIDE B)
In the menu you can select if the Clock Ref should work for Video or Audio.
In another menu you can switch Digital data to off position.
And thats what these indicators tell.
Not related to MUSE, as these options are always available in the menu.
Tho to be honest, I never touched these options. Just never needed to.

EDIT: Meh, someone was faster