Is there any way to use hexadecimal colour codes instead of using RGB colour codes to make colours?
make a hexadecimal-to-decimal convertor 
I did think about using that, but it is too much, I am using like two thousand colours.
Make a mathematical procedure to convert rgb to integer color.
Show how you use these 2000 colors, then we will advise something that will optimize the procedure.
and here is your procedure (should be draggable). Will work with 6 digit and 8 digit hex colour values
Example usage:
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