So this has been changed in their newest release 2.0.0.25 (not sure if it's publically available), and while the credentials are no longer in plain-text there are a few things you lose the ability to do.
Namely to tell if any given used is logged into a device, and secondly to sign in/out as a user on any given device.
I've provided my feedback to Yealink and hope to hear back soon. Neither of the above 2 issues are deal breakers, as the bigger goal is to be able to set configuration options, screensavers, time servers etc and have the user deal with the login.
Especially since the "Web Sign in" functionality is so simple, there is little reason to need the ability to sign in for a user.