Obviously I don't know the exact structure of your site, but I can't see any difficulties with SEO. I doubt any content behind a password would be found, the only thing to consider is the login page, depending on the use you could block it in robots.txt.
I think mostly Google see subdomains as different sites, depending on how they are linked together. You want to be careful that people can't publish spam on the subdomain this could hurt the overall reputation.
If you want to completely stop Google crawling the subdomains you could implement HTTP basic authentication, This loads before the page is even visible.
