Hmmm, where shall we start? The vanilla bean is brown/black. An extract made by dissolving something that is brown/black in alcohol is not going to be clear. What does that tell you? That's right, clear vanilla extract is not really vanilla extract.
Most manufactured foods can be modified to produce any number of desired attributes, and artificial vanilla extract is no exception. In this case it has been made clear, by combining propylene glycol or glycerin with artificial vanillin. According to Nielsen-Massey Vanillas, Inc. (which is in the business of promoting and selling real vanilla), "Artificial vanillin simulates one flavor component out of over 250 different flavor components found in natural vanilla. It is a byproduct of the wood industry or is produced from petro-chemicals." Not exactly a ringing endorsement!
The advantages of clear vanilla extract are that it doesn't discolor whatever you're making, and, like any artificial vanilla, it tends to cost about half as much or less as real vanilla. It is, of course, much harder to find, since it sells in such small volume. You might find it in cake decorating stores, but they themselves are fairly few and far between. For almost the entire population, your best bet for finding it is online.
Clear vanilla is almost only specified for use in a white icing, where even a little brown extract will muddy the color. Wilton Industries makes a "white-white" icing color, which uses titanium dioxide to whiten icings that are slightly off-white and to lighten the color of tinted icings. In our tests, it worked well to lighten a vanilla buttercream. The buttercream – made with butter, and therefore quite yellow at first, and just a touch darker once we added the vanilla – never made it to white though, and we used about half the bottle, or a whole ounce for only a cup or so of icing. It more or less gave the impression of being white, but it would not seriously fool anybody.
In any event, you certainly do not need to use clear vanilla extract for a chocolate icing – adding a little brown color to something that is meant to be brown is not going to hurt it. Once again, we have a case of a recipe writer specifying an ingredient that is just plain stupid.