What To Do in This Case?

[md_doc]

I am planning on starting an article directory. All the content would be 100% unique and original. My question is that I am planning to have a clickbank hop link on almost every article. How does google look at this? My site would have more than 10,000 pages. If I use no follow tags only for the affiliate links would it affect my rankings? Also is it recommended to use a no follow at all? Would like to get some input. Thanks a lot in advance.

[BigAlReturns]

I'm not familiar with how ClickBanks hop links work, but if they're like many advertising programs, the links are inserted with javascript, not plain HTML. If this is the case then they'll have no effect on your SEO, as the SEs can't read any but the most simple of JS.
If they are raw html links, then probably adding nofollow is the best course of action. A link to a big advertising program is unlikely to be seen as a link to a bad neighbourhood (which would incur penalties), but you never know. Even if it's not, it's still leaking PageRank out of your site unnecessarily.
Nofollow has no negative effect on the SEO of your site - Google will simply ignore the fact that it's a link, and read the anchor text but not see it as a link. You're safe to use it wherever you feel necessary, with no fear of penalties. In fact, it's probably best to err on the side of caution, and use nofollow where you have even a small amount of doubt about Google's opinion of the page you're linking to.