look, i'm not a themer and i don't know for sure, but you don't know for sure either. you are guessing as much as i am.
anyway, i think you were a tad harsh.
the menubar can be textured and coloured as you like with the extras.rsc file. i had a peek and it looks like (2028) Root Menu Caps, (2029) Root Menu Fill
control the menubar. i could not, off-hand make it transparent.
i think the reason why it does not appear to be readily available is because while most of the Windowing of OS X is flexible no one ever thought they wanted a clear menubar and thus, such a function was never built in, unlike regular windows where you can turn the opacity all the way down.
the reason you see as clear (i believe anyway, i'd have to see it again to confirm) is because the finder isn't running to show anything there.