You can drill the windows, but you have to be very careful. The vinyl windows are chambered... the bottom chamber needs to be sealed.
The supplier of the window might have a cross sectional cutout for you to see how it's constructed.
One trick I used to do was drill the contact bit all the way through into the wall; then, I drill a 3/4" hole saw through the top layer only. That makes it easy to get the silicone tube tip down to the lowest point of the vinyl window chamber to make the seal around the reed switch shell. I'd then fill in the area up to the top surface of the internal window sill with white silicone.
You're going to see the silicone around the contact, since it will be sitting in the center of the 3/4" hole. Make it look clean.
The ADT salesman is correct in warning you about this situation.
Be aware that the warranty for your window MAY BE VOIDED if you drill them through the bottom sill.
Nuts is right, don't silicone the weep holes either.
