Depends on the roles assigned to the ships. Ship roles are actually very powerful. Depending on a ship's role, it will preferentially target other ship roles, so you can build escorts covered in defenses and they will tank the damage while lightly-armoured gunships pound the enemy unmolested.

According to shiphullstatdefs.xml, it appears that the larger the ship, the less natural acceleration it has.  That can obviously work against you if you have a mix of ships however.  Besides other typical modifiers, I dont see any relavent differences between the ship classes.

However, it looks like it would be quite easy to mod in a natural jamming capability for each ship hull, making smaller ships more difficult to hit than the larger ones....which makes a bit of sense. That could make smaller ships a bit more relevant in the mid game, where usually its large ships that rule space.  Of course, this would make carriers even more ridiculously OP....

Excellent point. I would love to see thrusters increase the dodge rate of the ship as well as the speed.

On one of the weekly dev streams, one of the devs suggested that the current speed of the ship does affect how often it gets hit. I have not seen anything suggesting that in game however, so if it exists, it must not be a very big effect.

I am a beam boy.  I just like the way they look.  Therefore, to help reduce the Range advantage from enemy missiles, I try to put on thrusters so I can close the range gap more quickly.  Or, another tactic is to build your beam ships as interceptors.  They are practically in range with their beams right away.

True about an interceptor having high speed to get to the support ships, however you have to nearly destroy all of the other enemy ships before you begin to fire on the support ships.  I think its better to keep all of your ships together, and destroy each enemy layer, one at a time.  Like I said, I put ALL of my ships as interceptor (except MY support ship(s)), just to close the range quicker, due to the start locations based on ship class.