Some of it can be seen by the eye such as Troll Eyes, Chloroplast Skin, Hand & Foot Webbing, or other things that appear on the outside.
The majority of it is harder to notice. More then likely security will not shell out the huge cost for a scanner that can detect them. This means a lot of bioware will be unnoticed until the security has reason to know they're augmented already, like observing extra-human feats. By this time they likely have the guns drawn, but if you don't want to shoot you can have them give the characters biopsies, those would reveal bioware.
There are a few other occasions where bioware might show up on a scan. Like for instance Tailored Pheromones could reasonably show up on a chem-sniffer, provided the sniffer was set to detect it.