Ironically, colortable sub-folders will be seen by Autocad. If you have c:\colortable set as your path with 1 ctb file and create a sub-folder c:\colortable\temp and have 12 colortables in this folder, Autocad will see 13 colortables. Strange, but it does work this way at least in 2002, 2004, 2005 and probably 2006. Not sure about 07, 08 or 09.
Another option that you might want to play with is shortcut directories. Place these shortcut directories
in a set path location and see if Autocad looks at the shortcuts placed there as well. I've played with
that in the past, but don't remember what it did...
Pieter