Can the version of Hugo in the alternate timeline (the one where he's CEO of the chicken place) see dead people? I don't remember him ever seeing dead people, but I've been watching this spread over a long time period...
There was no "alternate timeline." There's only one history in Lost, and it appears to be immutable.
The "sideways flashes" from season 6 were not an alternate timeline, they were an afterlife constructed to help the Losties deal with their issues. So that Hugo sees nothing but dead people. Same with everyone else there.