It is a huge deal and has been since Google stopped passing referrers for signed-in users last October. That's because...
1) If it's a privacy thing, then Google is happy having a leak by giving these terms to advertisers
2) The data is not provided in a way that can be used by third party ad retargeting terms, giving Google a competitive advantage
3) Publishers can't use the data to better target with landing pages
4) Google Webmaster Central data only goes back for a short period of time, and if you haven't constantly been downloading your data, all your historic traffic information related to a term has gone poof.
This is a massively huge deal for attribution of organic search.
The queries you can download from webmaster tools are just 1 column of data....nothing to tie queries to conversions or any meaningful metric.
If it was everyone who was losing this data...I could understand the change but if you buy adwords ads, you still get the referral data even in https Google.
This isn't a huge deal as you can still get details of Google Queries using Google Webmaster Tools: http://www.google.com/webmasters/