Removing the case certainly changes the direction of airflow, but at the same time it isn't going to do any damage. Believe it or not some of these high end parts still end up in "normal-user" computers and they're lucky to have two case fans.
If you start getting random BSODs and restarts, then you should get worried.
"Nagi, how do you feel about being 'normal'? Normal means that if you leave something alone, it just remains that way forever. So if you can't stand that, then you have to be "not normal" in some area... - Seiichi Kirima's dying words