Am I stepping on any known sci-fi cliches I should avoid?
Hardly. Most of the people won't be surprised even if all alien captions would be in english, so they don't pay much attention to what alphabet it's written in.
On the other hand, if you want this to be "hard scifi", you should thing about poor aliens who will be forced to read these symbols. I mean, before making pictograms just as creepy as possible, remember that their main purposes is to be distinguishable from each other and to be easy to draw by hand (or whatever limbs these aliens have).
We, of cause, have some hard-to-draw alphabets ourself (chinese for example), but the most common is a way more simple latin. And if at some point our spaceships will fly into space to conquer other planets, it's captions will be undoubtedly in latin.
