in all actuality no window is "placed" into the tray. the tray is nothing more than a toolbar just like the ones on a window or dialog. An application adds a button to the toolbar and when clicked (as well as other events) sends a message to the windows procedure.
Just because theres an icon in the tray does not mean alot fo resources are being used nor does it mean the application has _any_ windows at all. The only requirenment is that a process has been started (note a worker thread can also create an icon but has to be started from a process)
mIRC could add support to place windows into the tray but it could become very thick very fast. Imagine being in 10 channels all minimized except for the 10th one. I wouldnt want 9 icons in my tray.
The ability to add an icon to a hidden process (appears as tho its in the tray) can be valuable. Sometimes i minimize mIRC when im working in VS and I have alot of applications open. Even with button grouping the taskbar can become full quick. At least thats one more application not taking up real estate on my taskbar