Or can you only find these items in crates and such?

On an unrelated note: do silencers reduce weapon damage?

It's rare, but they do drop them. Weapons can (it's random) also be dropped by enemies attacking the sector you are in ("enemies nearby"). Medkits, toolkits, along with a few other items, are only dropped by specific enemies in certain sectors. It may be as rare as once in a whole game.

Silencers do not affect damage.

Thanks!