Are there shuttle buses still running from Zhengzhou Airport to East Railway Station?

Well, there is no direct shuttle bus that can take you to the East Railway Station. Thus you are advised to take shuttle bus line to get to Civil Aviation Hotel first. The operating hours are from 08:40 to the last flight arrival. The ticket fare is CNY 20 per person. After arriving, take a taxi to the East Railway Station. The cab fare is around CNY 25.

Bus line 3 from airport to the railway station is operating hours to last flight?

No, the operating hours of this bus line are 09:00 to 21:00 from the airport to the West Square of the Main Railway Station.

To east railway station or the main railway station from civil aviation hotel, which place is nearer?
and price by taxi from civil aviation hotel?

The Main Railway Station is the nearer one. The distance is around 4 miles. If by taxi, the cab fare is CNY 15-20.

Can you advise if I take subway from airport to railway station at time 9 pm? Is it easier than shuttle bus?

I recommend the shuttle bus. But if you unfortunately miss the last one, subway is OK; the only thing is that it needs 2 transfers, one more than the shuttle bus+taxi.