The referral tracker has no effect on the link - but there are some sites that won't take the link with the tracker in it.
Let me give you my short list of good sites to link to:
Best Reviewer (they won't take a link with the tracker)
I still link on Myspace
...and that's about it except for "niche specific sites"
I'm nobody around here - and my earnings seem to prove that, but I do make money.