With regards to the shielded cargo, yes it helps (not guaranteed) to pass the scans. One of the skills helps as well if I recall, and you can also purchase (same places as shielded cargo) scan jammers that help even further.
So if you have it like me then you have a 90% chance to get through the scans with contraband. Unless you forget to transfer it to the ships storage, if you have it on you then you will get busted.
With regards to costs, you can play around all you want while in the ship builder, you only pay when confirming the changes at the end. And the biggest tip I can give, save before you change your ship, just in case you end up hating the interior or something.
A few reviewers for ship building said that the Scan Jammers and Shielded Cargo does not stack.
I wonder if they are right or not. I was under the impression you use one or the other but not both.