On the notifications page, it clearly refers to only browser-based and email alerts. However, disabling them turns off in-app alerts. That is a very different thing from browser alerts and caused me to lose a month of notifications in Aha.
Should be a simple language tweak to specify that this is for in-app notifications only.
In fact, there should probably not even be a way to turn off in-app notifications since it's core functionality. Just give a way to eliminate all of the notification duplication.