Yes - the upgrade to Atlassian account will also affect logins for the desktop apps. As long as you have a relatively recent version of the app (4.29 is the latest) then you should be automatically upgraded whether you log in via the web or via the desktop app.
For the immediate future, the transition won't require old clients to upgrade to Atlassian Account. They can still use their regular email and password. At some point in the future, however, the upgrade will become required and users will have to log into the web to set their password in order to continue using the clients. The clients themselves should continue functioning as normal after the upgrade is completed though.
We don't have a hard timeline, but the forced migration process likely wouldn't happen for at least a few months. Depending on exactly how old the client is, it's possible that it might not require any action on the part of users (we've changed behind-the-scenes authentication methods a couple times in the past few years). In the worst case, users might get a "bad password" error and need to reset their password on the web to get back to chatting. As usual though, we definitely recommend updating to the latest version of the client to have the latest security updates and features.
All good things come to an end - thanks to all our customers and partners who have been along the Hipchat and Stride journey with us. As of Feb 15th 2019, Hipchat Cloud and Stride have reached ...
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