The airport bus to Guangzhou Station will be running; it runs till the last arrival.
That said, Guangzhou Station is not a great area. At night or during the day. There's a 24-hour street with small restaurants and such about a 15-minute walk away, but I wouldn't send you there unless you're desperate to escape the airport.
You might look on the booking sites for a place near the airport to stay for a few hours. I recall there are a few.