I know EMD did produce some of the "early" GP models with short hoods that were generally only made with High Hoods. I dont remember if the GP9 was one of these models, but i remember that the model im refering to was made for a low number of railroads, possibly only one. If memory is correct, i believe that the locomotives were dark in color. I believe it was the Southern Pacific.
There have been LOTS of GP9s rebuilt with lower noses for improved visibility. Sometimes classified as GP9m or GP9r. Wether or not GP9m was in the EMD catalog or not, i cant say.
I know some GP9s lasted through the Chessie era and in to the CSX era, but i believe the numbers they held started with a "0". I believed the walthers model was offered in YN2 paint, and id be very surprised to see a GP9M in the YN2 era that had actually recieved YN2 paint. You have to keep in mind that railroads dont paint things as theyre on their way out. So for a GP9m to have recieved YN2 paint, they would have expected it to last for a while, and these units werent new when CSX was formed.