I am wondering if there is a keyboard shortcut to respond to a notification.
E.g. you get a notification that a chat messages has been recevied.
Press ??? and it will open the chat window.
Same sort of thing with email, wifi connected etc.
No unfortunately not - notify-osd is specifically designed not to be interactive so there is no way you can interact with a notification at all, including clicking it, or activating it with a key binding etc - see the NotifyOSD wiki page and in particular the section on rationale.
Actually there is...
If I understand you correctly and you use pidgin for example, then the notification icon will turn green when you received a chat message in pidgin. So just go Super + M, and that will select chat/mail notification.
So then you can select the person that contacted you and reply.