This depends on the application in question.
If the application spawns separate processes for the GUI and for it's internal use, then killing the GUI will only kill part of the application.
GUI applications usually have a Quit button, so if you have to kill it per se, then there is already something running wrong.
The Apache web server, for example, is known to spawn a lot of processes (also called forking).
Contact the developer/distributor of the application - maybe it's a known bug or something like that.