I also had the transmission replaced in my 1999 V-6 Accord at 18,000 miles under warranty. When backing out of the garage the transmission would emit a loud clunk after about 20 feet [sometimes]. Both my salesman [who is an ex-service manager] and the dealership service manager told me that a disproportionate percentage of these V-6 AT's require service. Rather than open it up they were advised by factory service to simply replace it. Have had no problem with the replacement transmission.
Have owned 5 Accords and this is the second where I have had trouble with the AT. My '94 LX 4-door required a replacement transmission at about 20,000 miles because it downshifted momentarily into first [rather than second] after making "vigorous"right turns at intersections.
Honda is very good about fixing "out of warranty" items, expecially if the car has been serviced regularly by an authorized dealer and you can provide documentation.