Not all of them have identical armaments. Pre Gar/Tambor class boats have less than 6 bow tubes, and this makes a whole lot of difference during the attack. Also, there is very little difference in conning towers in the beginning as well. Later in war when conning towers start to get refitted for lower silhouette, that is when the boats look at their best IMO.
Besides that, there are differences in top speed, and of course, the most important one - crush depth. Balao and Tench will give you much more manoeuvring space down at 450 ft, than Porpoise at 250ft IIRC.