Not 100% sure but I took a quick look at k3b
's sources and it looks like it uses the console apps directly - since they're even described as "external applications" in the comments. You should take a look at the sources yourself - C++ isn't really my game and neither is Qt so the code isn't completely clear for me but you shouldn't have a problem with it. It's pretty well commented too.
Pretty sure other GUI apps do it the same way - it's easier and faster to use ready-to-go, external apps - the developers can focus on the usability of their program instead actually rewriting an already existing app (as it would happen if they decided to use only the libraries).
I may be wrong, I'm no developer. Yet.