Why did a super-secret covert organisation have a uniform - one that lasted for over two hundreds years? Nobody noticed that in lots of hot political situations, people in the same uniforms kept turning up?
I would think that generic black leather would be a good choice for an S31 "uniform" because it's so generic that it can't be used to help build evidence against them. Is the Federation going to arrest everyone
with a black leather-ish outfit on suspicion of being an S31 agent? Everyone in the galaxy might have a set of black leather things in their closets.