Comment 7 for bug 1579415

With Muon, Sebastien actually meant Discover, which has the same problems like GNOME Software.

GUI applications should still be visible, and the fact that some are not shown is a bug in the metadata generator or (more likely) the packaging or upstream software.
Not all of these issues were addressed before the release, due to not enough manpower and probably not enough people caring about it.
See http://mhall119.com/2016/03/help-make-gnome-software-beautiful/ for how to report issues and fix things properly.
This should be sorted out for Yakkety, and some issues can also be fixed by stable-release-updates, e.g. the Krita thing would be a pretty good candidate, since it is highly likely a packaging bug.