This depends on where you are staying in Hong Kong and where you are going in . Where are the hotels in Guangzhou and Hong Kong? How do you go to the airport? What about luggages?
If you are near Guangzhou East Railway Station, take the Through Train to Hung Hom (or “downtown” Hong Kong, and transfer to MTR (HK subway) is a good choice. The train is more comfortable. Price is a little higher than the bus.
If you stay near or at one of the Guangzhou bus pick up points, Like Garden Hotel or China Hotel then it would not make sense to take a taxi to Guangzhou East Station to take the train. You can take the bus right from the hotel’s parking lot.
The train is more comfortable, The bus is more convenient, as they pick up in front of Guangzhou hotels and drop you off in front of your hotels in Hong Kong, which saves 2 taxi trips. The bus takes 3 hours. The train is faster but does not include taxi trips and wait time. In Kowloon, these buses often pick up and drop off in front of many hotels. Check with your hotel. Bus is best if the bus stop is at your hotel. You board and get off the bus right in front of the hotel, avoiding taxis and multiple lines at 2 train stations.
If you want to take the Through Train from Guangzhou east railway station to Kowloon, booking ahead is a good idea. You can buy train tickets at your hotel concierge or travel agent office, a small fee is added. I You can also take the Guangzhou East Railway Station to Shenzhen train (Shenzhen Luohu), then walk through the China and Hong Kong borders and get on the subway to go wherever you want to go, You may be taking a chance by not buying tickets ahead of time. The trains to Shenzhen run every 15-20 minutes and almost always have seats available.
From Guangzhou to Hong Kong you need to go through immigration regardless whether you take the train or bus. If you take the Through Train, you go through immigration in Guangzhou East Railway Station (China side, exiting), and Hung Hom Station (Hong Kong side, entering) Foreign passport holders are required to fill out the arrival forms. If you take the bus, you go through immigration at one of the border check points at the Shenzhen/Hong Kong border. It IS typically Shenzhen Bay Control Point. You need to alight the bus, go through immigration, and then board a different bus (run by the same company) on the Hong Kong side.
It involves getting off the bus, taking your luggage, and walking across the border immigration/custom check. Usually with a 40+ passenger bus. Waiting for everybody to get off and get their bags may take 5+ minutes. On the other side, you would be waiting for other passengers to get on the bus with their luggage. This process will likely take 30 minutes or more.
Hung Hom is a MTR station as well as the train station for Through Train. To transfer from the Through Train to regular MTR at Hung Hom, the rider enters the MTR platform after exiting immigration/custom, within the same station .