I submitted a case 743790 regarding a recent change in the email parsing that is breaking links back to NetSuite.  It seems that NetSuite changes any link/text that includes https://system.netsuite.com and changes it to some http://nsvirtualurl.com, which ends up breaking the link. 

The response I get is that this is as designed.  Sounds great, and I'm sure this is for a REALLY good reason.  I did find a workaround, which is to replace the / with the escape characters / (thanks support for this). 

However, this is a bit frustrating, because now I have to go through many many scripts/email templates to find all issues and fix them when they were working for a long time.  It seems that only half of the URL is being included in the anchor tag much of the time also see the example below. It is parsing completely wrong and causing a lot of confusion.  This example below is a task email that is sent (because setting send email in suitescript does nothing):