I am sure someone has, but quickly realized that it would be way too expensive and have a marginal at best impact on passenger throughput, and have a big negative impact on passenger safety.

Let me explain my thoughts.

1. Throughput, let make it simple, lets just double the number of people in a train, it is not realistic, but it is simple and gives the concept the benefit of the doubt. This means that the time to load and unload passengers will be increased sharply since it takes longer to get to a door, this reduces the total throughput of the system, so that you have to wait longer for the next train and wait longer for every station you stop at. But lets get to the next point to see if we can rectify this.
2. Cost, double decker trains are larger than most normal trains, so you need to build larger tunnels, and if you want to build a concept where you can board at both levels at once you need to build the entire station taller and fit dedicated ramps at a minimum. The cost would be significantly higher for this concept rather than just build a longer platform and fit more cars in. Now with double the ammount of passengers getting on and off the station, we need to build larger enterances/exits with more escalators bringing up the cost again.
3. Passenger safety, say that you are on the upper deck in a double decker metro train in a tunnel between stations, there is a fire and rhe train stop inside the tunnel, you are ordered to evacuate, in one scenario you are required to go down the internal stairs and evacuate on the bottom deck, this causes you to have to stand in line as others evacuate before you. In another scenario you can evacuate through all doors with ladders you place in the doors, you are about to climb down, but slip and fall, or someone knocks down the ladder, or perhaps you are the first to get to the ladder and as you try to get the ladder in place use it you accidentally hit other passengers outside already evacuating, all of this while the train is one fire and the tunnel is filling with smoke.

Single decker metro trains are enough, they bord passengers faster meaning they move faster along the system, they are less expensive giving more money to a larger system or newer trains, and they are less dangerous.