I can confirm that, have seen such, too.
Particularly with Midnight Commander not being shown.
My wild guess is that there is some (undocumented?) setting "Show only
graphical applications" or the like in Gnome or its derivatives.
Seems some bug just looking at the mere presence of a Terminal=...
Dear xdg members,
a Debian (stretch) user reported an issue where an application (freeplane) is
not
shown in the office section. So far I cannot reproduce this (GNOME3),
but the user reported [1] that it is "fixed" by this change:
--- /usr/share/applications/freeplane.desktop 2016-12-10
