First up, we don't use the term 'Hottentot' anymore. It is insulting, linguistically and anthropologically inexact, and hopelessly old-fashioned. (But especially the first one. Seriously, we don't use this term any more).
Throughout the centuries, any number of words have been used to refer to the shorter, lighter-skinned, funny-talking people of South Africa, starting with Hottentots, alternating with the even-less-PC Bushmen, later moving on to the much more politically correct !kung (who were one of the best-studied groups), the more accurate Khoikhoin and San (for the two main subgroups), the Khoisan (although this is primarily used for the language group), and various names that apply to specific groups.
But aside form all of that, Hottentot as a word is vaguely interesting, and certainly contested, (etymologically speaking). The most commonly-found theory is it refers to the odd form of their languages -- the Khoisan languages are full of pops and clicks; the '!' in '!kung' refers to an alveopalatal click, a click of the tongue against the roof of the mouth, right behind the teeth. This is one of the easier sounds to make. Based on this, the word is said to be a pun from the Dutch words hateren, to stammer, and tateren, to stutter. This was condensed to hot en tot, and a racial slur was born.
Other theories include that hot and tot were simply two of the more intelligible sound fragments that the Dutch settlers could hear in the local's speech, and the name is essentially echomimetic, or that the name actually comes from a Hottentot song from the Nama people, a song that Dutch sailors took to singing.
As it happens, the Hottentot were not done with their association with stuttering, as 'hottentotism' was used in the 1700s to refer to the condition of stuttering. It was used as a formal medical term, and was a step forward in the recognition and (perhaps) treatment of stuttering as a condition to be viewed medically (although I hasten to add that stuttering should not be treated medically!) As with Hottentot, the term hottentotism is now thoroughly dead.