Importing folder takes very long

You could write a script that would combine each of the files into one, thus saving Power Query some processing power for doing all this for you. When pulling data, it's best to try and do all of your data collection/transformations as close to the source as possible and this is an excellent example as to why. If this isn't an option, you'd probably have to stick with multiple queries to break up the processing for a possible performance increase.