Google's John Mueller said on Twitter that Google does not "pass signals through a lot of different kinds of links," when asked if Google automatically nofollow Amazon affiliate links.
He added "so I wouldn't be surprised if that were the case here," referencing the Amazon affiliate links.
I believe since before the nofollow attribute, Google probably had methods of not passing link signals from well known affiliate link patterns including Amazon, Commission Junction and others.
I suspect Google still has those methods but has added a whole deeper way of determining which links those are and handling it on a much more broad manner.
Here is John's tweet:
We don't pass signals through a lot of different kinds of links, so I wouldn't be surprised if that were the case here.
— John ☆.o(≧▽≦)o.☆ (@JohnMu) March 13, 2018
Forum discussion at Twitter.