I'm going to touch down in Pudong Airport from KL at 12.20 am

Yes, generally speaking, it's not necessary for you to worry about the safety problem.
From the airport, you can take airport shuttle bus line 1, get off at Hongqiao Railway Station. Then take high-speed train to arrive at Nanjing. The duration is about 1.5 hours. The ticket fare of first class seat is CNY230 and second class seat is about CNY145.

Thanks Kevin, but I meant to stay while for my friends' arrival. They are going to arrive at 11.30 am, while I arrive so early in the morning at 12.40 am. Is business center in T2 still open at that time? Or if I should stay at Hotel, is there any budget hotel in the airport?

According to your situation, you are suggested to stay at Dazhong Airport Hotel and take some rest.
Although the business center still opens, the fare is expensive than finding a hotel. The Dazhong Airport is just located inside the airport. You can find it easily.