You can fix the scroll bar issues with some javascripts and the http://www.iteurope.ie/clients/cart.php?a=add&pid=1 issue with go go .htaccess files. What does "lack of authentication" mean? The only real problem is bookmarking.
Ajax would be interesting, but i don't know how well it would work to embed whmcs in another page problem. Ajax would still have the bookmarking issue as well.
Why do you dislike iframes so much?
Iframes can be pretty useful to embed whmcs into a site that has alot of dynamic content and uses a cms like drupal. This way you don't have to theme everything twice and update everything twice.
Yes, SSL will work just fine in an iframe. The browser might complain about having some objects that are not ssl but you should be able to make your containing page ssl as well to correct that.