Deleting the maps folder wouldn't help load times, other than the defragging that happens (if you're using a HDD and not a SSD). The only other major hitch to loading times is the amount of folders inside custom, which every file that tf2 loads has to compare and check to see if that file exists inside custom (which, with a lot of folders, will add up. 10 or so folders doubles the loading times for me). Because most files don't get loaded at all most of the time, extra things being inside your maps folder and whatnot wouldn't reduce loadtimes any.
So basically reduce folders in custom (either by merging folders or putting things in vpk's) and defragment your tf folder (on a HDD) and you'll get good load times back.
eeeIt still has to catalogue them in some way I'd assume. When I ran a bind script with ~20000 lines it took an extra 15 seconds for the game to start for example.
They don't catalogue it. Big configs can cause lag also, that should be obvious when you get up to huge sizes, but no config ever should be 20000 lines big.