This is nit picking a bit. The lack of graves adds very little in terms of story and to be honest, this isn't theorizing, this is just noticing that the developers didn't want to waste time making hundreds or thousands of graves for virtual character whom serve no importance to the story. This is more likely a thread to increase your post count or something. And God knows what DekuLink's doing on this thread, so far he hasn't contributed anything noteworthy to this thread yet he's posted at least 7 times with one-liners.

This thread is ridiculous, you may as well be asking "How does Skyloft float in the air?" or "Where does the water for the waterfall come from?". Suspend you imagination for a bit! It's a video game for Christ's sake! For the sake of it though, let's just say the marked graves are those of people of significant importance to Skyloft and it's history, the other bodies are buried in unmarked graves.