Do not the mark main alerts/notifications area as aria-hidden.
Focusable descendents within an [aria-hidden="true"] element prevent those interactive elements from being available to users of assistive technologies like screen readers.
As can be seen in the code of PhabricatorMainMenuView, all three icons already define some $aural[] array to include output for assistive technologies, so their parent element should not block accessing that output.
Ref T16072