Well it's better to comply with Windows standards and install applications in the "Program Files" folder otherwise there may be complications later on.
Separation of application and data is generally a good idea, it's just that mIRC (like most applications I use under XP, commercial or otherwise) has always stored data with the executable; this makes it easy to backup, copy, or move the folder when necessary.
In any case, the next mIRC installer will move the contents of existing mIRC installations from the "Program Files\mIRC" (or wherever it's installed) folder to "Application Data\mIRC", and install only the mirc.exe in "Program Files\mIRC". Hopefully this won't be an issue for most users.
For users that want to run multiple installations, they will need to create a shortcut and specify a path with the -r command line switch.