I have been thinking about the same kind of thing, I won't have as many switches on the layout I am working on, but there are multiple ways to approach this:
1)Have the switches on a control panel that has a trace of the track plan on it, where the switches are located along the trace, so if you are moving a train towards a turnout, you know which button to hit
2)As you mention, have some sort of way of identifying the switches. Friend of mine did it by color coding, he had a colored dot on each controller (he was using Atlas Switches/controllers) and next to each switch he had something with that color on it he could see from where he was controlling it, he usually had some kind of small structure, like a storage bin or the like, with that color on it,you could also have a dummy switch stand with the color on it. You could also use numbers as you mentioned, and maybe hide the number in something that looks official,like some sort of sign, and use the last two digits to indicate the switch number in your case (so there may be an id sign board on the switch with a number like "90304220-01", which would be switch 1, switch 24 might be "43345333-24" to make it look 'official').
