I agree with everyone above's points.
Note that savage gantries have diminishing returns.
Stabilising cargo pods can be a good idea instead of hauling things back and forth, if you make a note of which system you left them in, and use their marker on the system map to get them back later.
Defence:
Taking a monitor or two with you might help defend freighters, as it can absorb huge amounts of damage, and has burn speed 10, and low maintenance/fuel.
The pirate Falcon has very high burn speed, and is a good ship overall for that kind of small fleet.
Lashers might make a good ship for the fleet, with lower costs than high tech frigates.
Storage:
Don't use the atlas, it's not very efficient.
The Tarsus is a normal Buffalo but better defended with otherwise equal stats, same fuel and maintenance costs.
The Buffalo (A), i.e. the hegemony auxiliary variant, has 1 higher burn speed than other buffalos at no cost.
The Colossus is great, it has a lot of storage, and the best efficiency for fuel and supplies, but has a burn rate of 7 although this can be upped to 10.
In terms of hull mods, unstable injectors will help freighters escape trouble, expanded cargo holds will be useful, solar shielding will be great if you happen to find some valuable objects very close to a star (which does happen), reinforced bulkheads will be useful if you aren't save-scumming and lose some freighters, militarised subsystems improves burn rate and removes maintenance costs from civilian hulls + certain hull mods, augmented drive field improves burn rate further, surveying equipment is important for, well, surveying, efficiency overhaul reduces fuel/supply usage a bit.
The Venture is also burn rate 7 but can be boosted to 10 too, comes with very strong defences, surveying equipment, and 350 cargo space.
The Apogee is another strong cruiser with lots of space and defences and some special exploration hull mod, and already has very high burn rate.