Human contact would have been possible (just like in UW1 and 2). I think it's just game design decision and a plot hole.

Why didn't Shodan just delete the player's save files? 

I'm kidding, OP does have a legitimate question. Shodan controlled the restoration bays. Survivors when the hacker wakes up could have the opportunity at some point in the plot to activate in their favor, but they were too busy surviving. Are you kidding, anyone still alive by the time the hacker wakes up must have been holding out in a storage room or some shit. The station is absolutely swarming, a true horrific nightmare if it weren't for the wacky music and ancient graphics. Nobody could survive that except the badass hacker and his badass cyberrig complete with deep hammerspace allowing for a one man army of 15 or whatever weapons and 15 instant-apply medkits.

They did try to activate them but were killed. That is in one of the early logs player finds.
When player enters Flight Deck level many of the restoration bays are now enabled by player.
Survivors should be automatically revived just as player is.

My headcanon is that, after seeing the mutant and cyborg hell Shodan was able to create, I doubt they trusted the restoration bays anymore.

Beat me to it. By the time you wake up the station is so utterly compromised because SHODAN was hard-wired into so much of Citadel. Everything more complicated than a light switch is suspect. A restoration bay would have been a no-go long since.

If you had seen your friends be turned into mutants by a machine, and someone told you that they had disconnected it from Shodan and they are all good now, would you trust them?

Not that they would lie, but we are dealing with an AI that has contingencies within contingencies and plans within plans who is always one step ahead of everyone.

I certainly wouldn't trust my life to that thing. I'd rather not come back than come back as... Something inhuman.

Fixed or not, the fate of the restoration bays is sealed for the survivors.

The interesting thing is, the player would have never seen the horrors in person and would likely know very little before their first death and resurrection, so it's reasonable that they would be more trusting. There's your in-game reasoning for why you're the only one using them.

Personally though I see them as bad game design (their only real penalty is lost time which is only relevant if you're playing in time-limited mode) so I generally find them too cheaty to use. So maybe I'm just scared of being a mutant too.

Be like trusting a teleporter, after you'd seen a friend get killed by one.

It's worse because a hypothetical teleporter death would be a mistake. In this case it's actively trying to kill you