Vent lines are located at the top of the bowl reservoirs. They are there to equalize pressures inside the bowl. Now way the bowls should be filled high enough to dump fuel, unless the carbs are upside down or you have a localized gravity inversion. perfectly normal to have vent lines routed to near the bottom of the bike.
In fact, you do NOT want vent lines to run up high, as dust and dirt would then trickle downward and enter the fuel bowl.
Maybe you are missing some important function assignments of the lines you are observing. Perhaps a picture of your concerned items might clarify.
Cheers,