Is there a way to monitor incoming calls that are routed thru a call queue to a particular extension rather than the direct line or is there a way to see if a extension is accepting calls via. the call queue or not?
As about accepting calls, you can check dndStatus in Presence API (this flag is set to "DoNotAcceptDepartmentCalls" if an extension don't accept call queue calls).
As about monitoring, the only way today is to match phone number from call notification. If it is a queue number, than the call came through Call Queue. But you will need to monitor individual queue agents anyway,