Much like how syringes, hand-to-hand and fiber wire were rather useless in Hitman: Blood Money because... well... you can make your Silverballers a pair of hundred-bullet assault rifles, and it's not that hard.
Exactly. Now matter how sweet it looks or how much more fun it is, people will instictively shoot instead.
Splinter Cell did it rather well. Where sneaking in is much smarter because your weapons have a very finite amount of ammo, the enemies aren't sissies and you actually need the guards to go on sometimes. I'm not saying AP should be the same, but there are a lot of different styles of gameplay that fit in the "super-spy" genre and they all have to look like valid options with none clearly better.