There are a lot of good answers here. In general, I think the best way to handle things is to let your PC's capture/interrogate prisoners. There are many approaches you can take to minimize the damage and even make it beneficial for your story. Here I've listed some approaches I personally take when GM'ing, and some examples from my most recent campaign.
First, you can always limit how much the NPC's know or can share.
A recent adventure I just finished is a good example of this. They were fighting a bunch of kobolds, and (being cowardly) a couple willingly surrendered after the rest of their group was slaughtered. The only problem? They only spoke Draconic. The PC's still managed to negotiate their surrender through body language and tone of voice, but could hardly interrogate them.
And even if they speak Common, nothing says that they have to speak good Common. some of my NPC's with Common as a second language speak such broken Common that the my players have to figure out what the NPC is saying before they can respond. I had another kobold later who said things like, "Leader big of self. Kobold help to human, Leader no see." (Translation: "Our leader is arrogant. If we help you, our leader can't know about it.") My players enjoyed translating and expanding to glean what understanding they could, though the kobold's Common skills were too low to say anything too complex.
Second, be ready to make up personalities on the fly.
The kobold with broken Common was originally supposed to be a "silent NPC" as you termed it. He was a dragonwrought sorcerer serving as the lieutenant to a baby dragon. I designed it as a straight-up combat encounter, and was surprised when the PC's immediately tried to negotiate instead of fighting (despite being assaulted by crossbows and traps through the whole dungeon). I had a loose idea of their motivations before, but as soon as the party started negotiating, I finalized why the dragon had taken a band of kobolds far from their usual territory, set up in that particular place, and had been harassing the local town.
Further, the dragon, which was mostly a plot device, suddenly required a personality. As a young thing, I made it naive but full of itself. "I am dragon, hear me roar! (Even if I'm the size of a house cat!)" The silent lieutenant (mentioned before), became the patient-yet-put-upon leader seeking to take the unreasonable demands of their child leader and implementing them through his own wisdom. He was sharp, despite his poor Common, and a shrewd'ish negotiator once the dragon dispatched him to do the boring part of negotiating. And yet, his faith in the leadership of the dragon never wavered, because that was simply the (semi-religious) order of things. For a kobold to not obey a dragon was inconceivable to his world view.
That gave me enough to work with for even an extended roleplay, and it just came out of the simple questions that I had partially fleshed out for the adventure already: "Why are they here? Who is in charge? Why do others follow them?"
Third, intimidation/persuasion/charm are not 'roll to get your way'.
To escape the combat encounter with the sorcerer and dragon, they had to make a series of about half a dozen various persuasion and intimidate checks - each one enhancing the effects of their roleplay - until they had established that they were willing to negotiate, that fighting them would probably be a bad idea (despite being at a tactical disadvantage, unknown to the players), and (very importantly) having played to the dragon's ego. Despite some generally high rolls, if they had said the wrong things, they could easily have caused combat instead of avoiding it (one insult and that would be all she wrote, unless they got a natural 20, which would only have negated the penalty).
Another example, from an earlier adventure, was when the fighter intimidated a scholar to get an important piece of (divine) information out of him. The fighter didn't scare the scholar nearly as much as the gods themselves, so it was doomed to failure from the start (especially since he was their ally, so he knew deep down that any threats were empty, probably). However, with a very high intimidate check, he basically choked up and just completely blanked out.
Applied to your game, for prisoners, who are they more afraid of? The party who might kill them, or their boss who'd make them eat hot coals (and then get really nasty)? Unless the party can convince someone in such a situation that they are willing to do worse than the villains, important information can easily be withheld for that reason. Which brings me to...
Fourth, Charm is not all powerful!
All Hypnotic Pattern does is Charm the target(s) (and incapacitate, but that's not relevant to interrogation). A Charmed target (1) cannot attack the charmer, and (2) the charmer has advantage on any social ability check. It doesn't mean they're under truth serum. Someone who's afraid of being tortured to death for betraying their leader is still going to be silent, no matter how good of a friend is asking.
They may even simply be too loyal. If you know the combination to the safe at your workplace, are you going to tell that to even your best friend in the world without a very, very good reason? (And the more likely that others will know it was you that told them, the less likely you'd probably be to stick your neck out.
Well, I hope that helps!