There's no reason for a screener to be reading the contents of documents while doing an administrative search for weapons, explosives, and incendiaries. Why someone wants to keep their information private is their own business. Period.

If you catch them doing it, summon a Supervisor (3 striper). If the Sup doesn't provide relief, an LEO should be summoned.

I don't think I've ever sent more than a dozen CDs in my bag through the x-ray, so I'm not sure what 50 will look like on the x-ray screen. I would group them into four Tyvek (FedEx or Priority Mail) envelopes and keep them in your bag when you send it through. If they do trigger a bag search, the environment where that takes place is much more controlled than the entrance/exit of the x-ray so you can keep an eagle eye on them. Would they want to know what is on the CDs? In all likelihood probably not, but if they do, read my first two paragraphs. Lather, rinse, repeat.