ESCs beep disregarding you have CC3D connected or not. If they don't I would check ESCs. Do ESCs have small led that lights up ? Are they getting powered ? If ESC don't have reverse polarity protection, and you connected battery wrong way they will fry, if they do have a protection and you did connect battery wrong way, they will not work (no beep).
I don't think there is anything wrong with CC3D if you can connect to it via USB. Also ESCs are not sending anything to the flight-controller, they only receive, so connecting them wrong way, shouldn't in principle cause any harm. Unless you connected battery the wrong way.
P.S motors usually don't beep, unless they have built-in ESCs ;-)