I read alot of threads about the tranny as well and it is popular on a 6th gen, but the question about how many people had problems with the tranny against how many didnt still remains. Its just that you only hear it when they have a problem but they dont tell you when its running fine.
What I personaly think what kills a tranny is when you drive like a NASCAR driver and try to go first on every light. Alot of my friends got Hondas and particularly Accords and none of them ever had any problems with the tranny. I used to have a 2000 which I totaled and now got an 03.
As far as your original questions, get a 98 or 99 and if you want to enjoy your ride, go with the EX and if possible, a V6 cause you will have to keep it for atleast 2 years so why not put a little bit more money and get a nice car so you can actualy enjoy it rather than thinking what if.