I know this question was asked a few months ago but here's more clarity and detail. "Awards" don't give you anything but can be earned repeatedly, and they are unrelated to bonuses. Bonuses do upgrade your character and they do stack, but any particular bonus from a mission can only be earned once from that mission. Some bonuses are easier to get than others, but to get all of them in any given mission, you have to earn the rank of Super Spy by collecting all the intelligence items in one go for that mission. The best way to check which missions you've done this for is by looking at the results screen that appears when you fail/die or complete the mission. It tells you the highest rank you've ever achieved for that mission, how many intelligence items you found this time, and the total number of items in that mission. You can get the Super Spy rank in any mission that has at least one intelligence item, which includes some of the mission briefing or training levels.
As for quantifying what the bonuses are, health and armor bonuses increase your total health or armor by 10 points respectively, but there seems to be only one health bonus. So you can only get 110 health but up to 160 armor (150 in non-GOTY versions). Ammo bonuses increase how much ammo you can carry for your weapons. I think accuracy, damage and stealth bonuses do provide increases, but the game doesn't say how or how much, and it's hard to measure or tell the difference. Accuracy may decrease the time it takes for the crosshair to shrink after moving or increase the auto-correcting of shots, such that if you don't quite aim exactly at an enemy's head, it may still hit and kill them. Damage may make your weapons do more damage, and stealth may make it take longer for enemies to notice you or make your footsteps quieter, but the Fuzzy Slippers item may help more with the latter. This would be similar to what these upgrades do in NOLF 2.
While the Reputation Bonus doesn't do anything, it is related to or obtained in the same way as some of the intelligence items. By choosing the more polite responses in most of the conversations you have, it gives you a hidden intelligence item that is needed to obtain the Super Spy rank in that mission. This means you can't skip those conversations if you want to get the Super Spy rank and all the bonuses. There are also other types of hidden intelligence items in a few missions that are achieved by fully completing certain objectives. Some earlier missions even require bringing gadgets that are obtained later in the game to get some of the intelligence items. Picking up Security Passes again after using them is another item counted in the total.