Both sides have control over which links should be rewritten. Publishers can add exceptions to exclude some merchants from link rewriting. Merchants can remove specific or groups of publishers from their affiliate program.
Skimlinks does not change the markup of the page. Only when we create the affiliated url for the links. In that instance we do not add nofollow to links.
With regards too crawling, we do not change our behaviour in any way for robots. Keeping links unchanged until clicked upon allows us to run in a fast and unobtrusive way. We do not slow down pages by running unnecessary code. Showing the destination URL improves user experience. This instead of unfamiliar redirecting url which users are less likely to click on.