You're probably correct in your diagnosis of a congestion problem in your nose or throat. No one knows you better than yourself. Maybe you have a deviated septum or larger than normal tonsils or uvula. There might be a surgical solution. If you can you breathe better through your mouth maybe you could try pinching your nose closed at night with something like the clips swimmers use and see if that changes things.
Speaking of finding true causes, let me tell you about a somewhat humorous diagnostic problem that I had recently. I bought a small house about 6 months ago. After I moved in, I started hearing thumping sounds that seemed to be coming from inside the walls. The sounds were especially loud at night and it went on for hours. It was hard to localize the sound; it seemed to be coming from everywhere, not from any spot in particular but it was very regular. I thought it might be plumbing noises like water hammer or heating pipe expansion. I shook every pipe in the house hoping to stop the noise or at least hear some change but couldn't find any pipe that seemed to be the noise source. The sound was so regular that I thought it might be a fan with a bent blade or a motor with a bad bearing but the sound continued even after I turned off all electricity to the house so I had to rule out that source.
After a couple of months I came to think that the sounds were due to thermal expansion and contraction of the house framing and considered calling in a structural engineer to see if there was a solution to that. I asked a couple of friends if they could hear the noise when it was loud to me but they said they didn't hear anything and that my hearing was probably abnormally sensitive. I decided to try recording the sound so I could turn up the volume and demonstrate it to a structural engineer. To my surprise I, couldn't record the sound even when it seemed especially loud to me.
Then one day I was scratching my wrist and noticed that the sound was exactly in time with my pulse. My heart occasionally skips a beat and the sound I was hearing stopped for one thump exactly when my heart stopped for one beat. I tried that test about 50 times and that convinced me that the sound wasn't coming from the outside but from within myself. The fact that nobody else could hear it and that I couldn't record it also pointed to that conclusion.
It turns out that I have a somewhat unusual form of tinnitus caused by turbulent blood flow in the carotid artery that excites my ear drum and mimics thumping sounds from the outside. I'm in my sixties and the tinnitus came on with advancing age. I would swear that the sounds are external but they aren't. I suppose our brains are so used to processing signals from our ear drums as coming from the outside that it's impossible to perceive the signals otherwise. It's comforting to know where the sounds are coming from even if there isn't much I can do about it. From this experience, I can see how some people think houses are haunted. At least I know I didn't buy a haunted house.