@grishka the subway system was initially started by two competing companies, Interborough Rapid Transit (IRT) and the Brooklyn–Manhattan Transit (BMT). The IRT used numbers and the BMT used letters.
When the city took over and merged the companies in the 40s, they had to keep some separation between the two systems since they were set up differently and couldn't interoperate super easily (track width, car and platform size, tunnel diameter)