Playing on the realistic setting I found myself dead many times from sniper fire when I never even saw the shooter. I would peek up from a hiding place and see myself dead on the ground. As far as hacking, I had the same impression as you, at first. In SS2, rare was it that you needed to hack when you were in danger. In Deus Ex, I found myself hacking systems only while someone had their back turned and often came out of the system I hacked confronted by gunfire.
Security too is in the name of balance.
If it were Fort Knox, the game would be insanely hard beyond the point of fun. If you had to guess all the passwords or use tools on all the doors and locks you would constantly be stuck due to a lack of tools. Again I recommend raising the difficulty. The different between easy and realistic is quite astonishing. Finally is your problem with item distribution.