A couple of thoughts:
1) It does seem likely that shadowrunners are going to get stopped once in a while. If the normal way SINs are handled is an opposed test between the scanner and the SIN, then those stopps are going to blow up very badly. For game-play reasons, I don't like that
2) In SR Missions, in the Denver series, they give explicit rules for border crossings. Now, whether the following rules make sense or not, I don't know. But if borders aren't using SIN scanners, I don't know where they would be used.
The test is a threshold test by the players, of Charisma + Etiquette + SIN Rating. The target is a variable number which I would interpret as the Scanner rating. And they allow a teamwork test for the part.
As I say, I don't know whether that rule is realistic. But it has the advantage that the players get to roll to determine their fate. And most of the time, the players will succeed. If you declare that the border is on alert, up the target number. (Border patrol upped the sensitivity, knowing they would take longer and get more false alarms, but detecting more problems as well.)
Yours,
Joel M. Halpern