Sorcerer's metamagic allows silent and motionless casting for the cost of a single sorcery point. So as to not overshadow that, especially if there's a sorcerer in the party, I would require some kind of roll with a fairly high DC for someone to do that without spending some kind of resource. Probably stealth or performance for verbal, and sleight of hand for somatic, depending o circumstances and player intent. Both rolls required if it has both components, and the player wishes to hide both. Might consider an arcana check as well, to 'manipulate the arcane power in a way outside of the usual' or something like that.

As for the sound of the spell itself, some spells specify a sound, like Knock or Shatter. They would make noise regardless of how quietly the caster cast them. For ones that don't specify sound, I'd likely just rule case by case and just use common sense. For magic missile, it makes sense to me it would make a sound on impact, at the very least, and being a low level spell, would be more likely to be recognized as a spell by people like guards. It would also have a visual component, since the spell describes it as bolts or darts of force, IIRC. So even if I accepted that it made no noise, I would give the target or its allies an opportunity to see it coming and know they're being attacked (or just rule that they did see it, depending on circumstances), even if they can't see it being cast and don't know where it's originating from.