The idea behind the phrase "taken short" is that a person is caught by an urgent need to use the bathroom. Golding's use of the phrase "taken short" refers to the boys having unexpected bouts of diarrhea from eating too much of the fruit from the fruit trees. Piggy comments on this in the first chapter to Ralph; the fruit has disagreed with his stomach. Later, Ralph uses the phrase in one of the tribal meetings to explain why Simon was wandering in the dark alone; he says "he was taken short" to poke fun at Simon's odd behavior.
The phrase "taken short" and the phrase "taken up short" refer to a situation of surprise. When one is "taken short", one has been surprised and one's expectations have been contradicted, confounded, or otherwise proven false.
Often, these phrases are used to describe a situation where a person was prepared to speak, but due to surprise has to stop the act before fully starting. There is some literal meaning to the phrase, which we can imagine, however, the "taken short" can be seen also as a figurative phrase drawn from common speech.
Phrases like this qualify as colloquialisms, figures of speech that often have figurative meaning and come from common speech.
Colloquialisms appear often in literature since they provide a sense of actual conversation and use the pronunciation, grammar, and vocabulary of everyday speech.