Service from Shekou to Kowloon has ceased, but there's still service from Shekou to the Macau Ferry Terminal on Hong Kong Island.
This is the official site of the operator:
http://www.xunlongferry.com/e-pwzx.asp
Sailing times are 7:45a, 10:15a, 2:00p, 4:30p, 6:45p, 9:00p.