I think a small dose of well RP'ed inexplicable scariness is good.
Ever since mankind has ventured into environments such as the sea or the sky there have been inexplicable happenings.... why not in space?
No I don't think we should go all ghost-busters or have vampires and such....
*imagines the Order flying to the theme-song of Ghost Busters....*
But legends and scary stories add to the complexity and depth of the Freelancer universe.
Why does it even have to be supernatural? theres plenty of fringe-science possible explanations for ghosts. especially in a sci fi universe. (go watch a few of the wierder Star Trek's if you want inspiration.;))
As long as the people RP-ing the 'ghosts' don't try too hard to explain it, and as long as too many don't show up too often (a ghoul in every nebula) I think its rather cool :)