How to protect trade secrets on board with SMD components?
I find it extremely unlikely that your product could contain 'secret' methods that can be implemented with recognizable discrete components. If anything, actual innovative design that is worth keeping a secret is at least done on the chip level, but more commonly on a process level. Things that can be implemented with discrete or at least non-custom components are most likely just obvious designs.

That being said: you're not going to have any legal force by keeping stuff secret. This is exactly what patents were made for. You don't have to increase the cost of your product and screw over the customer with unnecessary protection measures and on the other hand you get the complete right to deny any of your competitors your technology. Otherwise they'll know there's something juicy in there, reverse engineer it within .4 of a femtosecond and hide it in their products. Even if you find out, you have no way whatsoever to stop them from using the same not-so-secret.