I gave you the reason.
No amount of 'design' can overcome simple physics.
Okay, yes the longer ships are more vulnerable. But the thing is we don't know if the typical forces war ships experience is enough to break this longer, thinner warship. Take for example long pencils. These pencils are more vulnerable than your average pencil, however, the routine forces it undergoes in serving as a pencil isn't enough to break it. It's only when you start subjecting the pencil to forces it was not designed to handle, like breaking it over your knee, that the pencil breaks.
For the warships we don't know if making them longer is enough to enough to overcome the integrety of the materials making up the ship during manuevers and combat. If the ship could be lengthened and still do everything a ship of shorter length could do why would the engineers make it wider for the sake of forces the ship is not going to experience? If people wanted to build ships for maximum durability they would all look like spheres (or whatever the most durable object is).
Throughout the series we see a variety of ship designs ranging from more spherical to longer and thinner ship designs. The design of ships in the Mass Effect universe could very easily be influenced by other factors other than limitations imposed by the durability of ship materials. Maybe frigates are designed to have a certain width so the crew won't constantly run into each other in a narrow hallway. Maybe after the ship gets wide enough to easily facilitate the crew they just make ships longer to facilitate the length of larger mass accelerators.