Ah....The G.I. Dunno factor (AKA Combat Munchkin). I've run into this problem many times. Here a few quick suggestions for dealing with shlemels and other sorts of goof balls.
1) Make the enemy smarter: Sure, you have the Mook factor for your average guard, but in places that are important, here are a few dirty tricks I use to mess with players heads:
1) piezo-electric walls and floors: this is a security system via wich no scanning field is detected (looks like a background distributed power source) and relays the exact position of the players via induction to the security comptuer running things. Also, who says internal security phaser strips don't exist?
2) the claymore factor: static non-energy defenses, pressure plates under that nice soft rug, chemical explosives, armour peircing darts....lovely things that aren't powered, thus not readily detectable by tricorders. especially if the area in question is already sheilded. What, no engineer to think of things like this? BOOM. Too bad. oh...and put traps where they least expect it. BOOM. and jsut when they think you've trapped everything...slack off...make them paranoid...then put one under the villians bed. BOOM.
3) Give the villians access to better toys than they have. TR-116 sniper file anyone? Dominion-Class Transporters? nanotech grenades that disable they weapons power links? or...if you are feeling evil....borg nano-probes.
4) political fallout: let's face it. people likes things quiet. too much gun bunniness draws whiners. Whiners whine to superiors. Superiors Become Irrate. repeat as nessesary.
A brave little theory, and actually quite coherent for a system of five or seven dimensions -- if only we lived in one.
Academician Prokhor Zakharov, "Now We Are Alone"