It was mainly a stir in the clickbank community as there where a lot of clickbank members and if they wanted to buy a product that you where promoting they could change your id to theirs and then they received the commission. Don't get me wrong it can happen with heaps more affiliate links then just clickbank, just clickbank is the easiest to do it with.
Yes it is still an issue but I don't think it is crazy. I think you are better of masking your affiliate links so that they are more appealing to your visitors. For example
www.brelove.com/**name-for-aff-product** looks much better then
www.affiliate.com/?affiliateid=223462 or something.
You don't need any software to mask your affiliate link you can do it all yourself, all you need is to set up a redirect. Personally I use .htaccess redirects, this is a file located on your website directory and if it isn't you can create it. .htaccess is use to tell browsers what to do in certain situations (there is more to it then that but that is an easy way to try and explain it).
All you need to do is open .htaccess (or create it) and add
Redirect /name-of-affil-product
http://www.link-to-affiliate-website...i-id=1242..etc
this will make your address
www.brelove.com/name-of-affil-product redirect to the affiliate link.
Hope that helps, if i wasn't clear on anything just ask