from the Immd website:
Since 16 December 2004, the Immigration Department has introduced the automated passenger clearance system (e-Channels) to members of the public. All existing passenger control points have been installed with e-Channels, including Hong Kong International Airport, Hung Hom, Lo Wu, Lok Ma Chau, Lok Ma Chau Spur Line, Man Kam To, Sha Tau Kok, Shenzhen Bay, China Ferry Terminal, Macau Ferry Terminal and Tuen Mun Ferry Terminal. Currently, Hong Kong permanent residents (except those under the age of 11) or Hong Kong residents holding Document of Identity for Visa Purposes (DI) can use their smart identity cards to perform self-service immigration clearance. Since 12 September 2006, e-Channel service has been extended to people who have the right to land or are on unconditional stay in Hong Kong, and non-permanent residents who have been issued with a notification label. Since 18 December 2007, e-Channel service has been further extended to cross-boundary primary school students under the age of 11 at Lo Wu Control Point. From 19 May 2008 onwards, eligible frequent visitors can enjoy e-Channel service at the Airport Control Point. Meanwhile, please note that Hong Kong residents must bring along with them their valid travel documents when travelling.
So yes, the border crossings into China and the Ferry terminals in Hong (which contain the Hong Kong immigration control points you will clear to travel to China/Macau) have e-channel services as well...