Actually, I've used my modified zapper for COD-WAW on Bravo button configuration all this time.
I feel no disadvantage. I actually think that it gives me an advantage in terms of ergonomics and stability. (Probably why I like the M1A1 a lot

)
I only feel the disadvantage in MOHH2 bacause when I started playing, I wasn't aware that some control features were not available for zapper mode.
It was too late for me to switch by the time I found out.

For me, it was just a matter of getting used to pushing buttons on the Wiimote with my left hand while my thumb stays on the joystick to keep moving.
A bit difficult at the start but once you get used to it. It feels natural.