at what speed will the panniers be unsafe to ride on on a naked bike you think? since it creates quite alot of drag compared to a top box hence lifting the front up more?

That's why I install a top box
Imo it's the other way round. Panniers sticks out directly to the airflow while top box is blocked by my huge body so too box should be more aerodynamic.

Anyway, my commute to work is 10km one way and I ride a 999cc bike. My vote is to commute with big bike. The power makes overtaking lorries easily and can get you out of sticky situation if needed. Also big bikes usually have much better suspension, tires and brakes plus dual channel ABS so safety is much better than kapcais as well.

But then again, with great power comes great responsibility. The power can also get you into sticky situations easily as well if you aren't careful.