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Google Webmaster Tool is showing Less Link data for Home Page

Coinciding with the Google pagerank update another update seemed to be taking place silently. But contrary to the PR update It was a bit disturbing for professional SEOs and webmasters all around the globe. I noticed this when I was checking links for one of my sites in Google Webmaster tool (GWT) and found that the number of links has dropped from 91,000+ to just 30,547. Later I found that GWT was showing 50 to 70% less links for100+ sites. I was shocked and felt melancholic to see it as I did not use any disavow link feature provided by Google. Several thoughts came running across my mind (Of course most of were negative). A few of them were:

1) I thought Google might have flagged and discounted low quality links to my site. If this would have happened, I feared my ranking might have dropped too. But fortunately, my rankings were intact. I checked my GWT mailbox, too dreading a unnatural link warning but did not find any such kind of mail.

2) Second thought was that Google might have discounted no-follow links or old links. This hypothesis is still to pass through the litmus test.

3) Bug: Within my hearts, I am more than sure that this is a bug or a software glitch but waiting for some words from official sources of Google.

You can participate and report your dop in link numbers on Google Webmaster thread here.