Depends on the application. Most applications on windows will take the clicking of the red x to mean close the application. Others take it as a hint to minimize to the notification area. However most applications will give you the choice once and remember it from then on. KDE applications tend to take the minimize to notification area, gnome applications go away (but fear the one process gnome-terminal). Close should mean close.
Close to hidden is even worse – I’ve seen a few applications close to a still running, just hidden from you, mode. They run as a service while they’re in that mode, even if they’re not designed as such; it is a cheat for quick start.