On the CB400F (same carbs basically) those nipples have rubber hose that route up and over the rubber airbox (there's actually a metal tab/hose clamp thing they route through that is off the #2 carb slide cover screw) and down to the between the swingarm and the engine to drain under the bike. My guess is they're for allowing the fuel to breath or something for balancing.
I've never seen fuel coming out of them and with the vertical nature of the hoses, I can't imagine fuel ever coming up and over the airbox so it's probably for condensation or fumes.
There is a great cable/hose routing graphic floating around the web for the CB400F. I believe it's from the Honda shop manual, you shouldn't have any trouble finding it.
Any questions, let me know.
Rick.
Rick.