Shockingly, when asked point blank if affiliate programs that employed juice-passing links (those not using nofollow) were against guidelines or if they would be discounted, the engineers all agreed with the position taken by Sean Suchter of Yahoo!. He said, in no uncertain terms, that if affiliate links came from valuable, relevant, trust-worthy sources - bloggers endorsing a product, affiliates of high quality, etc. - they would be counted in link algorithms. Aaron from Google and Nathan from Microsoft both agreed that good affiliate links would be counted by their engines and that it was not necessary to mark these with a nofollow or other method of blocking link value.
But note the point they had not mentioned what will they do with low quality links.
From the above points it clear that Google will passes a link juice. But still many of us in affiliate industry uses a parameters and redirects in affiliate urls. Reason is just simple not all the affiliate are as genuine or reputed as Amazon. So if your links in 50 sites and may be 40 site can be those which Google does not like so links from those site may harm your site.
So as I said above its always good to save website's image while leaving some link juice.