I have just noticed that my P4P has a scratch mark, it may even be a (not very deep) crack. I'm wondering how much this will affect the overall working of the drone - is this something I need to be concerned about?

That will depend on what has caused the scratch - if its rubbed up against an object in your case/bag then probably nothing to worry about but if its a stress crack then I would ship it back

I would not be concerned about it. That close to the sensor it will be out of focus anyway.