One advantage to link cloaking is that you can switch out merchants without having to go find and change links all over your site. If you set up yoursite.com/bestairfare yoursite.com/hotels then if one merchant does not work out you can just change the link in one place - like htaccess or the cloaking program and all the links throughout your site change.
Example. I use
GoTryTHIS for all the client links on my site. They aren't affiliate links, I just use the program for tracking clicks AND also for convenience. So for example, check out the AMWSO link top right sidebar. That link is all over the place on thousands of pages of my site. If Chris ever wanted me to change the page I link to, I'd have a heck of a time finding all the links and it would take forever to change them. With GoTryThis, I just go to the interface, replace the link and it changes it everywhere on my site, blog, forum, directory, old newsletters, everywhere.
So if you had a merchant you heavily promoted over time, but then their conversions went south or they pulled their CJ program and moved to Performics, you'd only have to change the link in one place.
Warning though about cloaking - sometimes the way the cloaking works the tracking cookie won't pass, so test. Another warning there are "black hat" cloakers - in fact GotTryThis has a black hat version - I don't use and neither should you. They stuff cookies and use iFrames which are against the TOS for most programs.
In fact even in the WhiteHat version of GotryThis that I use, you need to be careful. If you use the option that asks you to add a link title - it then uses an iframe. I added a link title once, not knowing what it did and my client complained he was not getting hits from me because the link was iframed so he could not track any traffic I sent him.