Hi Sunny,
Your idea has merit, in that we should have a choice of passing the Effects through to the Sub outputs. I think Yamaha's thinking is, the Sub outs are mostly used to send a variable volume signal to an external mixer or effects unit. In that case, you'd want the signal to be sent dry.
As far as I know, the only output signal that carries the Genos effects are the Main outs. When I play large shows where there's a sound man, I run my Main outs to two Bose Pro 8 speakers. They each have a line out, from which the sound man can take a feed to the snake. My effects are completely controlled by me. I even tell the sound man to set the mixer channels on his board to dry (I think they usually do that for line level signals anyway). The sound man can still play with the bass, mids, and treble.