Dymero - 5:00 pm on Jul 19, 2013 (gmt 0)
I think the main question now is: is google considering subdomains as part of the main website? Do subdomains affect (positively or negatively) the main website?
Yes, they do, but this wasn't always the case. They used to count subdomains as separate entities, at least for the case of counting links. But almost two years ago they changed that to include subdomains links as internal links, like any other page.
There's a good explanation at the Google Webmaster blog: [googlewebmastercentral.blogspot.com...]
And Matt Cutts did a video last year about how subdomains no longer have a SERP advantage as they once did.
Subdomains affect the site because they're considered part of the site as a whole and not a separate entity. Until you fix the hacking issues, and take care of any extant hacked links (or at least document that you can't get the removed), Google probably won't lift the penalty.