Apparently in FL Vanilla, rep DOES determine whether you get scanned or not. There's a chart in the strategy guide:
+0.6 to +1.0 - Friendly, and a potential combat ally. Police ships won't scan you. +0.2 to +0.6 - Generally friendly. -0.2 to +0.2 - Neutral -0.6 to -0.2 - Generally hostile, but won't openly attack. -1.0 to -0.6 - Hostile. Ships will attack you on sight and bases will not allow you to land. -0.6 to +0.6 - Police ships will scan your cargo for contraband. Pirates will scan your cargo and potentially try to steal it.
