Well, normally, your missile defense ships would be set to protect the whole fleet, so who is detected first wouldn't change much. You could make a civilian Rock as mentioned above: a ship full of armor and CIWS. If it's large enough, it should be the priority target.
As for big vs. small ships, well, you need a bigger shipyard for big ship, and they take longer to build. Jump drive rapidly becomes prohibitively expensive. However it does have some advantages, like the fact that you'll loose less mass to armor for a given armor depth.
Well, If the Defense ships would be detected first then I assumed that They would be fired upon first and I could put extra shield/armor on them.
Though I guess having less ECM would only matter if they are not the biggest ship, according to what you say.
Jump drives, Shipyard size and time does not matter that much to me, If the ship isnt worse than small ships or break too easily that is.
I just want a fleet of huge juggernauts wrecking anything in the way, WH40K style.
The main reasons I do it are:
1. To save fuel.
2. To reduce the level of micromanagement.
1. I assume that one of the mining ships have enough cargo space for the mass driver and the rest lack said space. I guess that saves a little fuel depending on the engines and the possible freighters.
2. I send the freighters to pick it up at the time when I tell the miners to go somewhere else, A few clicks more but a minor thing.