I suppose that since some foreigners were kidnapped, the embassies feel they have to warn of this otherwise they will be blamed if it happens again ....If it does happen again they can say "Well, we did warn you! "
Given that the Philippine islands are so close to that area of Sabah, and that it has happened, I myself, think about it and wonder whether I would go to Semporna . Having said that, I go into Sabah often and have never felt nervous about being over by Sandakan at least.
Going online to the Borneo or Sabah Times may give some info about whether anything has happened recently ...though I haven't heard of anything .
Radio Australia at the time said three Indonesians were taken off a boat by Phillipine pirates possibly from the Abu Sayaf rebel group (Phillipine)
This is from CNN online in 2005 when Australia updated their warning..
."The warning noted that in April 2000, international and local hostages were taken from the Malaysian island of Sipadan, a popular dive site off the south-eastern coast of Sabah near the border between Malaysia, Indonesia and the Philippines.
A group of 28 alleged kidnappers linked to the Abu Sayyaf terror group based in the Philippines have since gone on trial in Manila for that attack, in which 21 people were held hostage until ransoms were paid.
Further kidnappings occurred in September 2000 from Pandanan Island, in October 2003 near Lahad Datu on the eastern Sabah mainland, and in April 2004 at sea off Sabah's east coast. "
A diver's (CDNN )site tells of a kidnapping off Mataking island in March2005
There is an article in the Sabah Times 12 June 2008 about a journalist being kidnapped - but from Jolo island...again - not far from Sabah....
Perhaps security has been tightened and this is the reason for no more (news of) problems in Sabah. I believe also,that a number of islands that used to have overnight accom no longer have it - said to be for ecological reasons, but.....