I can connect the two lightguns and the trackball up on my modular panel (all USB).
The only problem I've had is that with them all connected I sometimes have to remap the "mice" (all three appear as mice) in the analog controls menu (noname-mame or Analog Mame +). This can be a problem as in my setup it does not seem to remember these settings for a particular game. Therefore the next time I find myself doing the same mapping again.
There may be some way around this in the software, but I'm not sure what it is.
I've gotton around this by just unplugging the trackball from the USB hub when I want to play with the guns. Also, for some reason the PS2 mouse does not interfere with the light guns, so another alternative would be to wire the trackball to PS2 and the lightguns to your USB ports.