If you want to launch an app already minimized, you can use the powerful, but woefully underdocumented Haiku utility "hey"
For example, I have BeShare in my /boot/home/config/settings/boot/launch folder. But I don't really want to see it the moment I boot up. I want it to share my files as long as possible, but I'll actually look at it when I need it, or when I have the time.
Here is a way to start it up minimized. Well, not really, if your computer is slow it will flash on the screen briefly.
edit /boot/home/config/settings/boot/UserBootscript. Right at the end insert the line
hey BeShare set Minimize of Window  to "bool(true)"
"hey" is case-sensitive and every space counts. You may need to experiment with the value of the sleep command if you have a fast machine.
Now BeShare will launch, and then immediately be minimized.