Water in door
Hi, Most car doors are built with weep holes in the doors and yes they get clogged. Any grit or dirt on the window will go into the door and clog the weep holes. I never lower my windows if they are dirty or wet. Even in the rain I just open the door rather than open the window. There are rubber seals on the outside of the window at the top of the door, but the windows are not flat and that seal cannot follow the curve of the window. So dirt, dust, lawn mower debris all goes into the door and eventually clogs the weep holes.
I take care to use compressed air to clean the weep holes as often as I can. I just did not get to it on my 97 Avalon. Mom bought the car new and it was garage kept until I got it. Mom used say if you can's afford a garage you cannot afford the car. She is right. Mom passed away in 2013 and I got the car. So the car was not exposed to dirt getting into the door. Also the car only had 42,900 miles on it, even today it only has 75,000 mi on it.
The other day I went out to the car and opened the back door and found the sloshing sound. I took a wire and cleaned the weep holes and got a shower.
So the answer to the water in the door problem is exactly as you said. Cleaning the weep holes is a permanent fix, until dirt clogs them up. So get your compressed air, a pizza box to lay down on, and blow all the weep holes in all the doors. I took the door panel off and found there is no way to clean out the weep holes from behind the door panel.
Sorry for making this so long, but I see I am not the only one with water in the door so I very relieved that I found others had this problem and fixed it the way I fixed mine.