You also have to keep in mind that the production of the 6-speed was somewhere around 2700 models for the 2003 year. I believe they have sold around 2000 of those.
Manuals are not very popular at all except with a select group of enthusiasts. Those enthusiats would most likely be looking at other companies... and if they are looking at Acura... they'd probably be looking at the RSX-S or the NSX depending on their income. I have a feeling that there may be a chance of a 6-speed in the TL... but I wouldn't count on it for sure....