Depending on the era and the particular film, silent film may have had a leader (A length of film used to help the projector get up to speed and ensure the film is threaded correctly, before the movie proper) but it probably wouldn't have been the familiar "countdown timer" which was created among other things to ensure proper audio synch.

"Sepia" in photography is itself a colour "toning" technique that was widely used. Silent-era film would often make use of colour filters, and in later films it was common for different colour filters to encode information about the story (See for example Griffith's Intolerance, an early example of multiplotting where the different plots, which are only thematically related and don't interact at all, are each given their own colour filter). The silent film era is vast and comprises over 30 years, thousands of movies, and dozens of different countries, so depending on the place, time, and film you would see black-and-white films, colour toned monochrome films (With sepia being one common tint), colorised films, and even early colour processes being used.

Most film prints even today will have a leader on them with these numbers. The countdown was never intended to be visible to the audience. It's purpose is to assist the projectionist in loading the film properly into the projector.

Silent films ran at 18 frames per second, and the speed was increased to 24 fps with the advent of optical sound tracks. The numbers change every second, so there's a number every 18 or 24 frames. This way when the projectionist is starting a film they can see the film going into the projector and know how much time they have between when they start the motor and when they activate the audio head and the lamp shutter just after the last leader frame ("Picture Start" frame) goes through.

More modern projectors which are designed to be easier to load or even those that are self loading will start the image as soon as the projector is started, thus the numbers would be visible. Before the advent consumer video products, if you wanted to watch a movie at home it was on film. If you recorded your kids at Disneyland, it was on film, and if you had to watch a training film at work or something educational at school, it was on film. The leader running through self loading projectors or those who just didn't bother to start it on a low number would appear on screen, which likely led to it being associated with all old films.