It sounds like there were two things that might've happened with that GM there:
1) The GM missed something, like Reaver said. There's a lot of moving parts, a lot of characters, and a lot of things to keep track of. At most tables I've seen, gear management is something that the Players are supposed to keep track of themselves. So, if the GM told the players they were limited to some sort of gear, the Players acknowledged that, and moved on, then it's easy to see how the GM would have missed it later on.
2) The GM was playing favorites, and it's something to worry about. But that's a pretty serious accusation and not one to be made lightly.
To answer your questions: A Skin Pocket would make things harder to find during a standard visual or tactile search most definitely but, as others have said, sensors would go right through it. It's just like with subdermal cyberware. MAD Scanners can detect that stuff easily, so they can detect things in the pocket as well.
Theoretically, the MAD Scanner would then catch anything that it's capable of sensing in the Skin Pocket, but the key here is that the GM can only call out what's detected if they know that the Player is intending to bring it in. If it's not mentioned, the GM can't do anything and usually assumes it's not there. This is one of those situations where the GM and the Player have to work together to make sure the rules work out.