Err.. the cigarette's purpose is mentioned in the instruction manual. It's not some big secret. But who reads manuals these days, right?
Anyway, I have a couple of issues with the scoring mechanics:
Random weapon drops from boxes, wounded allies, and enemies means you'll have to restart the checkpoint until you get the best weapon for the highest possible score in the area. This is tedious and boring, the exact opposite of what a score based action game should involve.
If you are playing for score, the death penalty is meaningless when you can exit to title every time Sam dies. Although there may eventually be a trick where dying to replenish your ammo is worth the 1000 point penalty, assuming you can't just keep reloading to get the ammo you need from boxes or enemies.
The developer credits mini-game is long, boring, and counts towards your score so you must play it every time. This is a tedious barrier to anyone hoping to play for score, and it frankly smacks of egotism.
Finally, given how important the time bonus is towards your score, I'm surprised there's no option to display your current time and how much time bonus you'll be getting at that moment.
Looks like the developers at CAVE are still one of the only console developers who know how to put together a proper scoring system that doesn't involve tedium these days. Better luck next time, Platinum Games.