Great question — answering as the UphillTech team:
From Google's help document about links to your site in webmaster tools : Not all links to your site may be listed. This is normal. I've seen many webmasters complaining about how incomplete this data is. Googlebot does follow links through 301 redirects and even passes Pagerank across them. Links through 301 redirect should show up in the link report according to their help document: Link counts now include links redirected using 301 or 302 redirects. When links don't show up, it is probably worth doing a little more investigating. You may want to check the following: Is anything in the path blocked by robots.txt . Either the place where the link is located, or the URL that does the 301...
Full answer by Stephen Ostermiller: https://webmasters.stackexchange.com/a/55738 (CC BY-SA 3.0).
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