You’ll need several hundred secondary weapon kills to get the weapon mastery achievements anyway, so you’ll get this eventually if you’re a completionist.
If you’re a stealthy player you don’t typically get a lot of secondary weapon kills, so you may need to be more aggressive than you otherwise would.
As far as weapon choices, I prefer the Welgun and the Thompson, but none of them are particularly bad. Experiment with different guns and attachments, and find your favorite.