The boundary layer acts as a "bubble" to the aerodynamic structure of the aircraft. It covers a small distance adjacent to the body of the aircraft, where velocity is reduced to zero(at the wall), up until free stream value (outside vortex). In other words, it is a region where a change in the airflow will not affect the airfoil and the surrounding air distribution.
I agree with Buff in that the windshield wipers would be protected by the boundary layer. Most of the air distribution in front of the aircraft will be deviated by the vortex created by the aircraft's nose, preventing a disturbance from small structures like that.
However, in the case of a take-off or a lifting force, that layer is very small and can be neglected, so if the wipers affect anything, it might be at that time. Even if it does, I reckon it is a very small alteration.