I'm a command line junkie, and I don't think command line apps as a general rule should be listed in the visual application manager.

Now that said there might be some exceptions, for example things like VIM, nethack, or other CLI apps that stay open and provide a constant interface. You can create a shortcut to these in the ui, and that can be helpful, and not necessarily confusing to end users. But they should be clearly labeled as the hardcore/niche/geek tools that they are.

But any app that you invoke on the command line with parameters, and no additional input, should likely be left out of the Visual App Manager.

I don't see how I could complain that I had to go to a terminal and use the apt-get command to install something like latex commands, or flac encoders etc... that they are certain to invoke from a terminal/script anyway.

It's not possible to show critical update notifications graphically even for non-graphical packages?

It seems like this sort of problem would also exhibit itself in critical updates for library packages?