In general, I don't think search engines have any problem with redirected ( I don't call them 'cloaked') links. For evidence, just look at most of the top coupon sites.
...people can steal your commission if your affiliate links are shown. Also, many resources say that site visitors are more likely to click on a link if the long, affiliate link doesn't show in the bottom left of the browser.
On the other hand, from my limited testing, I've never seen much difference in results between using straight, or redirected links. I guess any small difference is worth taking advantage of tho.