The use of scanners has puzzled me slightly too.
In build mode they seem to be activated as soon as you link up a module to the scanning computer, what can result in running out of power immediately while building. I presume this is a glitch.
In flight mode you can add the scanner to the command bar and with a right click charge it. Why one would want to do this more then once puzzles me because a blue rectangle indicates that it is active / charged already and it stays that way even when leaving the ship and coming back to it later.
As for what it does, I only noticed a blue message box from time to time telling me pirates where on a scavenger run nearby my location, but, for instance, it doesn't tell me that there's a shop within 4 or, if in a owned system, 6 blocks away.
As always, if not mentioned otherwise, this all is in single-player mode.
Greets,
Jan