I definitely do not count it against them as long as they know how to human at the interview. I just review the code as I would any repo.
The only thing is that with regular projects I tend to go “I noticed on your GitHub you have project X that uses technology Y, etc etc”. With H projects I just go “do you have experience with Y” and let him choose how much he wants to share about the project. So far they remain vague on the non technical details and I let them leave with their dignity intact.
So, ranked, way ahead of candidates without visible projects, but slightly behind people with projects we can discuss in detail in front of the people from HR ;)
Bare repos with multiple users are a bit of a hassle because of file permissions. It works, and works well, as long as you set things up right and have clear processes. But god help you if you don’t.
I find that with multiple users the safest way is to set up/use a service. Plus you get a lot of extra features like issue tracking and stuff.