When looking through the art directory I noticed that there are flavor grpahics for units in BtS that never showed up for me - for example, a native american war elephant, asian maceman etc - they never showed differently for me, yet they are in the art directory, why is this?

there are quite a few things also in Vanilla that were never implemented - often unfinished art files - but that were left in the release files. I assume for the benefit of modders...