My gut feeling is that system design questions are not off-topic per se - they're a class of best-practice questions, which I recall a while back we decided to be more tolerant of.
But it's still perfectly possible to write a system design question that's off-topic for other reasons. For example, in my opinion:
What's the best way to design an online auction site - too broad
What's the best design for a home media server - not about managing information technology systems in a business environment
What's the best answer to this interview question - this is a hypothetical, not a concrete, issue
So, if you actually have a real system to design, and you've done your homework and narrowed things down to two or three options, but genuinely can't decide which one's best, then my personal feeling is that there might well be an interesting, on-topic question there. I can't speak for the community, though.