Yes, as a past seller, and collector, while dealer, Gold and Silver were the two pen choices for signatures on big cards. I'm not talking about $1 to $3 dollar cards, only ones that truly have lasting impact on the game. Say, like a Timewalk. Force of Will has that impact.
As for the color choices, it's because of preference when you're collecting and dealing these cards. The pens usually are done with a heavy ink (Sharpee) and soaks into the paper. It will not smear, scratch, or wear as quickly as others. Mind you, this is based on that most of those colors are used in Sharpee's or other good brands.
Secondly, the color comes out more when you see them signed in that color, as opposed to a red, blue, etc.
-Houts-