Google doesn’t care if all your links are nofollow or not. The important thing to remember is that Google does actually “follow” the links, they just don’t pass PR to the landing site.
As for the cloaking question, there really is no difference in click-thru rates IMO. The link a user is clicking on can look clean as in http://www.casinosite.com, but have the affiliate code behind it. The user is going to click on it anyway, and many of the affiliate codes redirect to a clean URL anyway, so to the user it is a seamless process. I wouldn’t assume that most surfers pay attention to the URL anyway, or care what it is, there are tons of dynamically driven sites out there today that have all sorts of crazy looking URLs, people don’t stop using them.
If you do cloak the links in Javascript, Google definitely won’t see the link and you won’t leak PR that way, though I’m not sure that’s much of an issue anyway. It would be interesting to test out however.