In modern movies, it's not too much to ask for futuristic spaceships to get equipment and programs that can detect even small traces of unknown and potentially hazardous life- forms or other biological material. Back in 86, I'm guessing it either couldn't be conceived of, or was purposefully left out so another movie could be made.
In any modern film, Ripley would've done a ship-wide scan of some kind before going into cryo. That didn't happen in 86, and we can't blame the past for ideas they couldn't imagine. I've given up on that.
The thing is though, would they have been able to do anything about it regardless? How many eggs and facehugger were there? Would the facehuggers have gotten them even if they were not in cryo? They may very well have been looking at a similarly awful fate aboard the Sulaco, even had they known there were aliens onboard. Full size warrior aliens are one thing, but those facehugger are some agile and quick little buggers. All they'd need is a millisecond.