Sure there is... 1. You're not broadcasting to all the search engines your site is an ebay affiliate 2. It looks better when visitors scroll over links and don't see ebay url Thats my view about it.
1. Search engines don't really care, many top organic ranked websites (SEO) have un-cloaked affiliate links. And not everyone is an ebay affiliate. There are thousands of other merchants in CJ. 2. The javascript links have mouseovers that look like javascript:CJ('28NKSK39UFSNK'); - the OP isn't talking about mouseovers, he's talking about the full javascript links.