How should I safeguard my FAA certificate number?
I guess the question is, what can someone do maliciously if they have your certificate number, and what's the risk of that happening?

My assumption is that they can do nothing - and therefore the risk is zero - because no one uses the number for anything: it isn't needed for medicals, training, TSA approvals, flight reviews, checkrides, renting aircraft, buying insurance etc. People do want to see your certificate (and even take a copy) for various reasons, but no one will accept your certificate number by itself as proof of anything. That's my experience in the part 91 GA world anyway; I have no idea if certificate numbers are more important for airline pilots.

So my guess - and it is a guess - is that this does indeed come from when SSNs were used as certificate numbers. And as a result, unless your certificate number is also your SSN, there's probably no reason to do anything special to try to protect it.