Some things on foot just don't work exactly the same way as they do in your ship and I think this is a good thing, a lot of the time. In fact, I'd prefer it if more things were like this (such as taking out a target silently not applying a bounty against you unless detected).
If you wish to scan a target for a bounty then do it when they cannot see you. It's not a problem if anyone else sees you, it's only important for the target you're scanning. But, I am pretty sure that you'll only get bounty targets if it's an anarchy settlement. So you can just shoot them and scan them afterwards for even more safety. Only, of course, then you don't want to get seen doing it unless you want to get into a fight.
Finally, if you disable the settlement alarms, no alarm is ever raised irrespective.