You mentioned that you have problems with shooting. It sounds like you haven't invested many points into your weapons skill. Two upgrades makes any weapon class good enough for combat. If you attach a laser mod to your stealth pistol, you'll have a much better time aiming too as the bullet will travel to the laser dot. You can find your first laser mod on the very first mission. The second one is in Hong Kong, but you have to explore a bit.

Don't stress yourself over trying to find every little secret. The simple fact is that you won't, not on your first playthrough. In fact, you will miss out on a lot of things. And it doesn't matter. Luckily, the game is very replayable.