Remember, the author of the article constructed a scenario where, it was expected that the "main" function ends up treating an empty "CONFIG_DIRS" input as an uncatchable IOError; in other words, an empty array was invalid/not-allowed, per the rules of this program. Depending on the context in which you are operating, you may or may not have similar rules or requirements to follow.
Empty lists are actually generally not a big deal - they are just lists of size 0, and they generally follow all the same things you can do with non-empty lists. The fact that a "head" function throws an error on an empty list, is really just a specific form of the more general observation that: any array would throw an index-out-of-bounds exception when given an index that's... out of of bounds. So any time you are dealing with arrays, you probably need to think about, "what happens if I try to index something that's out of bounds? is that possible?"
In this particular contrived example, all that mattered was the head of the array. But what if you wanted to pick out the 3rd argument in a list of command line arguments, and instead the user only gave you 2 inputs? If 3 arguments are required, then throw an IOError as early as possible after failing to parse out 3 arguments; but once you pass the point of parsing the input into a valid object/struct/whatever, from that point forward you no longer care about checking whether the 3rd input is empty or not.
So again, it depends on your scenario. Actually the more interesting variant of this issue (in OO languages at least) is probably handling nulls, as empty lists are valid lists, but nulls are not lists, and requires some different logic usually (and hence why NullPointerExceptions aka NPEs are such a common failure mode).