I believe you are missing out on some XP if you do not unlock items. Sometimes containers do have some useful items. Early game, you may find some good stuff. Most of the time it is just junk.
I see a lot of people that bought the PS3 version saying the unlocking is really quick. I have no idea myself (I play on Xbox) but I assume it is similar? On Xbox, you have to press the buttons soon after they flash on screen. Press all the buttons that flash (typically 3-6 button presses) and you unlock the item. I assume that is how it works on PS3?
The best advice I have seen from someone is to place your thumb (or finger, whichever you use to press the buttons) in the middle of the button pad. Then stare at the middle of the button prompts on screen. If you see the left button prompt, press the button to the left of your thumb. If the top button prompts, then press the button above your thumb... you get the idea.
Other than that, maybe the prompts are just quicker on the PS3 than they are on Xbox. I have no idea. If you have enough omni-gel you can always unlock a missed decryption with omni gel, although note that the number of items in the crate you are unlocking will never give you enough omni-gel to replace the omni-gel you used to unlock the crate.