To summarize for me, my points are valid. Silent Running alone should be enough to avoid scans from security ships, on account of the risk one takes at messing up their approach and colliding in the mail slot and taking hull damage instead of shield damage, as well as the heat build-up that risks damaging internals. Failing that, there should then exist a utility mount that can actively blind scan attempts (give it a 20 second cooldown, to be fair) and/or shielded cargo compartments/passenger cabins that trade reduced capacity for scan immunity. Finally, VIP passengers should only get upset if a scan succeeds, not just because one started.
The only time when i was scanned happened when i misjudged the time to dock while docking to an outpost, while having a dude on my tail, dead set to scan me.
I was so sure i will make it.. but then again, the NPC managed to scan me half a second before docking - 7 VIP passenger missions failed in that last half second
Anyway - it's really simple - the game does not offer a 100% out of jail card. Where is the fun in that?
So while silent running (or popping heat sinks) helps, it's only a part of the solution
My way of doing this? I dont even do Silent Run.
I just approach the station so i drop off from supercruise just in front of the mailslot, then drive straight in, no auto dock as speedy as possible (up to 200m/s if getting a pad in the back)
Make sure you request/cancel the docking request till you get a Landing pad in the back (40, 10, 25) - but never in the front row or close to front row (24, 9, 39, 32, 2, 17). Picking a pad in the back allow you to get in (using a large ship - Cutter, Beluga, Conda) at high speed, minimizing a lot the chances to get scanned.
*(just watch the starport image on your left (target) hloscreen and align so the entrance is oriented about SW - or 7.30 if you prefer the clock indications)