Hand off the management of Web Applications to GNOME Software
From a semantics perspective, the removing of "Applications" should be consistent for all types of applications regardless of the source, so that when people go to try and remove web applications they're looking in the place where they remove packaged applications, etc. meeting their expectations for how it should work. Without the need to know about the Web Application Manager.
Also, since the "Web Application Manager" is only for deleting web applications, this behaviour could easily be picked up by Software.