Hi kwblue,
that’s an interesting question.
The first type of linking is good to track hits. You have 2 links to for each site: the 1st one is not search engine friendly and I would not accept a link exchange with you if my link is managed by that script; the 2nd link is a straight link and is search engine friendly.
As long as you have both links on the same page there is no issue. And there is no issue because you ALSO have the straight link in it. But if you use only the link with the script it would certainly be a issue for your link partners.
I think there are some scripts you can use that are more search engine friendly. For example, the script I use in my website has the capability of counting all clicks on every single link of my website. I know if people are reading the article about Acropolis Casino more than Cirrus Casino, I know on which links they are clicking,….