Not everything in the repositories is run from the GUI. Many applications
are run from the terminal and as such would not get an icon or menu entry. I
have used Ubuntu since feisty and I install lots of applications from the
repositories and from outside sources and it is rare that I would not get a
menu item. In fact, so rare that I can't remember a single case.

I have had this happen temporarily when an application did not completely
install, but when I finished the installation then I got a menu entry. In
these cases, I run the application from the terminal and look at error
messages that are generated. Then I troubleshoot these. Sometimes you need
only to sudo apt-get -f install. Sometimes you need to look at broken
dependencies and find what other application might be causing the problem.