Getting back to the question of apostrophes in alien names and languages... I'm proofreading my new story for Analog right now, and it features two alien species, one of which has apostrophes in their names, the other of which does not. I started to second-guess whether the apostrophes were really necessary, but I realized that they help to differentiate the one species's names from the other, which probably makes it easier for the readers to keep track of which weird names belong to which characters. So maybe that's part of the reason so many SF alien languages are heavy on apostrophes -- because it's a handy visual hook to distinguish them from other alien languages. Although in that case, of course, it only works if you don't use it with too many species. Also, I think the apostrophes help suggest that the aliens' speech sounds are sharp and staccato, as well as making their consonant-laden names more legible.
In fact, come to think of it, the apostrophe-using aliens in my story have gender prefixes rather similar to the Andorians', although they're capitalized and there are only three of them, Ch', Kh', and Sh'. And it's coincidental, since as far as I can tell from my notes, I came up with this species' naming scheme in 2000, less than a year before the novelverse Andorian names debuted in Avatar. (This is an old, unsold story that I recently rehabilitated.)