Have some reasons:
1) When someone else gonna use your computer, the peoples doesn't turn off the amule because its daining all the band...
2) Hide the program in work from the boss..rsrsr (for someones)
3) If you dont want the others know the program is runnig/what you are downloading
4) dont fill the systray.
5) increase the features of amule, making it better and different from the others.
Otherwise i think it must be implemented like an option in tool's menu, not an imposition of the program.... use this feature who wants... let the option to turn it on/off! So, if the user wanna use, turn it on, dont wanna, turn it off...
I read above about daemon...thats it...this is the name of the file thats allow the apollon hide in the system...
Have some way to add this feature in the amule???