Which clues are you referring to? Care to elaborate?
I think he dies as well. By the end, he had stepped on a lot of toes and made too many enemies.
The very first episode of the season they call 6a, there is a poem that they recite as they re-introduce all the characters. It's like the seven souls that leave your body when you die. I googled it, and it's by William Burroughs. As each character appears he talks about another soul. I took it as a sort of introduction to the end of Tony's life. Like Chase was announcing out-right that he's gonna die.
Meadow is introduced as the guardian angel. She is the one that calls Tony out of the coma and prevents him from entering the house to die. She isn't there in the diner to save him in the end.
Also, I noticed that while Tony is sitting next to the lake, he becomes annoyed at the bell ringing on the boat. This scene originally drove me nuts. Why was he getting so ticked off, and WHY weren't they explaining it?? In the end, right before the blackout the bell on the diner's door rings. I thought maybe the boat's bell was a premonition of his death, which is why it disturbed him.
There's a man in the diner billed as "man in member's only jacket". There is an episode earlier in the season titled "Members Only" where they make fun of a guy for wearing that jacket. The guy winds up committing suicide because Tony won't let him leave the mob. I think that points to the guy in the diner being a little more important than just a random extra.
Besides the obvious conversation between Bobby and Tony about in the end you don't hear anything...it's just the only ending that makes perfect sense. The loose end of the up coming indictment doesn't matter. No explanation is needed because Tony is dead.
My husband and I both originally thought along the lines that Tony was just paranoid, and we were supposed to feel his tension in that last scene. After watching it again, I don't think that's correct. Tony didn't seem to feel paranoid AT ALL. He sat in the middle of the restaurant and didn't even notice that guy looking at him? I can't imagine Tony not confronting someone he thinks may be a threat.
I don't think David Chase has ever openly said that Tony dies, but he did say that he wasn't trying to screw with the audience, and that all the answers are there. The most satisfying ending, imo, is that Tony died at that moment. It's really the only ending that brings it all together for me.