I have not encountered the situation where ghost players do not show up in the search. Well, maybe I was just not aware of that. In my limited playing time of OOTP, I have not seen the ghost player gets development change. Also, my assumption is that ghost players are career minor leaguer (see my previous posts) so they should never appear on career leader board. Players with sufficient playing time in the majors will be properly removed upon exiting the league because the player will be physically transferred from Players.dat to retired.dat. Anyhow, this is my first time to hear this. Don't have any comment and can't help you here. Sorry.
p.s. By the way, I am curious about something. Does the situation happen with the league has already been attempted fixing with utility or the league without the "touch" of utility. If it's the former case, it may be the utility that makes ghost players gone from searchable to un-searchable.