I dont know about the US, but in Canada V6 accords weren't offered with a standard tranny until 2004. The 98-03 model never came as a manual. The new 04-05 models come with a 6-speed.
As cool as as a V6 hatchback would be, how about this for a cool swap:
Take a 94-97 Accord V6 coupe body and swap in a H22A.....mount it at close as posible to the firewall as you can get. Since the V6 coupe's engine bay is much longer than the 4 cylinder's, it would pretty much be a Mid-engine, front wheel drive setup.....stick on a nice suspention setup and go race. Wayyy cooler than a front heavy V6 hatch (that thing would handle like a bag of boiled ass).