Good questions, and what I took from the episode is that only select people can see 'apparitions'. I want to believe the Producers here that they are not dead, but they certainly are pushing the regular audience to believe that death is the case.
Not to go against what you said, but Boone has shown up, with considerably longer hair... in Locke's 'hallucination'. I have a problem with the stuff Locke ate to hallucinate, I tend to think it's not real, but a placebo to get your mind going in that direction, does that make sense? I mean rose had her little quiet times in season 1, and we really don't know what was going on in her head at the time.

Basically what I guess I'm trying to say is that Jaob must have an idea of who is special or not and makes a list. Jack however, must be special since he can see his Dad. But we know ben knew Jack was a surgeon and needed him for his own purposes and most likely changed the list that Jacob made.

I don't think Jacob is dead, but he may have power like Walt but stronger, and is being kept against his will, hooked up to something maybe (Help Me) and that's why he hates technology.