The short answer is yes, but it has always been hard to match all referrals back to specific URLs. And for once, the problem is not just Google.
Encryption is already a problem
As most everyone who looks at data knows, analytics programs are definitely are not capturing all keyword data, since Google began encrypting keywords in 2011 . That encrypted keyword data is what is being reported as “(not provided)” in Google Analytics reporting. But Google has not encrypted data to the point where you cannot see the URL, only the keyword is being stripped out.
You may be familiar with a URL referrer called “None” or “Direct” or “No referrer” in your data. This referrer could come from apps, offline, and non-browser referrals to your site from anywhere (including, but not limited to Google properties). It is not the keyword encryption from Google and it is not a flaw in any other metrics software that is causing “None” referrers. The “None” referrer just isn’t recordable as a URL, because most Web metrics tools only track browser referrals.
However, there is another issue with encryption that may cause you to lose URL referral data. And as encryption becomes more broadly used you may start seeing more “None” referrals in your metrics. The way it works is when you are on a secure site (https) and then click on a link that is not secure (http) and the URL data is lost in the transfer from https to http.
Google has a solution for SSL search, but mobile and Safari searches may still be stripping out URL info
When Google decided to encrypt all signed in searches they fixed that particular problem with the https to http transition with Google SSL search because they really didn’t want us thinking that Google stopped sending any traffic to us, they just didn’t want to share the keywords with us.
But the problem still exists and complete loss of referrer info is a problem in some mobile searches using Google and Safari browsers. More info on this can be found at SEL: Safari Shifts To Google Secure Search in iOS 6, Causing Search Referrer Data To Disappear
So that is real problem — a loss of referrer URL data because of encryption — it is not a Google search problem though, except possibly for mobile and Safari. The unfortunate thing is I have always seen “None” referrer data in all the metrics I have monitored over the years and it is impossible to know how big a problem it could be when the source of None referrers is not trackable. But if you start seeing an unexplainable increase in “None” referrers you may want to investigate whether your site or your audience behavior is changing in such a way that encryption could be a factor.