I mean… he’s likely created several, so he’s got a good idea, right? He’s also determined how difficult they may be to find and all kinds of stuff.
You can never tell where the group will look or what they will ignore.
I once had an abandoned temple of Tempus, god of war in the Forgotten Realms. It had been abandoned in a hurry a long time in the past. When the group went in, I made sure to describe rusted metal to the point where some doors had fallen in, furniture had been falling apart, etc.
They party to the room where armor and weapons were forged and repaired. On a table was a +2 shield that had been left behind, forgotten in the rush to leave. It hadn't painted yet, so I described it as a gleaming steel shield that looked like new.
Many groups would have been like, "Wow! It's not rusted even a little bit. There must be something special about this shield." Not my players. They just looked at each other and were like, "Do you need a shield?" Nobody did, so they just left it sitting there and walked away.
Clues are like that. They will not look or ignore some clues, easily find others. And create clue via actions and questions the DM didn't think of that would have yielded a clue. You keep ignoring that last part, even though this is probably the tenth time I've said it.
THE PLAYERS WILL COME UP WITH THINGS THAT THE DM DIDN'T THINK OF. That means that the DM is not in control of the solution.
Doesn’t he have a ton of influence here, too? I mean… he created the NPCs. He will decide what they share based on what the PCs say. He’ll set the DCs for any social rolls.
Influence, yes. Total control over what happens with them? No.
What can they come up with on their own?
Seriously? You've never seen surprised by something a player came up with that you didn't think of? I'm highly doubtful of that.
What clues could exist that the DM didn’t place?
Lots of them. There are probably many things that would have left clues that I didn't think of. If they do, that's awesome. A new clue happens.