Makes sense when you think about it...
The drain below the windshield/screen is typically not far removed from the air intake of the HVAC system in a typical vehicle. I'd guess that there is a baffle to keep liquid from being spritzed out of the air outlets, but that's about it. The demand for air is satisfied by pulling it through that drain/vent grid underneath the windshield/screen. If you're using water for the washer unit and it's stagnant, there can be almost no doubt that bacteria will find its way into the passenger compartment through the ventilation system.
As far as bacteria growing in the A/C evaporator coil goes, consider the following...air from a wide variety of sources gets pulled in over that coil, bringing with it dust, pollutants and some bacteria. As most modern cars have tightly packed engine compartments (where the majority of the A/C and air handling components are located), a lot of heat builds up in there when you've stopped after enough driving to warm the vehicle up. The warm, damp environment inside the evaporator coil box is conducive to bacteria growth. That's why the air coming out of the A/C vents may be smelly when you first turn the system on.
The 1996-2000 Chrysler minivans have a big problem with this.
It's easy enough to stop this, however. About a mile before you reach your destination, turn the A/C off and let the evaporator coil dry out a little bit. Even on a wickedly humid day, the incoming air can still dry the evaporator just enough to help alleviate the problem.