I'm 26 hours into this game, taking it slowly, so still early-mid game. Most of my equipment are still Mk.3 or 4.
What I learned so far:
Speed is life. Faster ships can disengage when overwhelmed and kite enemy fighters to thin down their rank. Currently in Sturville and I doubt I'd want to 'upgrade' to a Destroyer.
Neutron Cannons are awesome; decent range and great DPS. I could tear up capital ships just with this, assisted by 2 Ion Cannons and 2 Partical Lasers.
Flak Guns seem to be the best Secondary. You can drop into a cluster of fighters and tear them apart.
Beam weapons are also effective against fighters.
With all those said, Baraccuda with Tachyon Cannons + Mining Lasers build may work out too, as they have the highest DPS.
My own build is Barracuda with all mining beams, emp flak, neutron beam broadsides, and mk6 shields (shields are OP). I recently managed to reach rank 8 in the trader's guild so I now have the large guild cargo hold (+32) and also the EMP ablation. I haven't used it yet but considering that EMP is the most annoying thing for me right now when running dead drops and cargo missions, it should come in handy.
Honestly I feel like the mining beams do most of the work and they're only mk3, the emp flak is a recent drop (mk6!) and is really nice against fighters if they get close, but it doesn't seem to do anything against missiles.
Well that's if I choose to fight, nowadays I only bother if I scan some juicy component in the big capital ships.
My current strategy is to go from system to system, to the trader's guild stations and take all the most paying dead drop missions, plus a cargo haul to the next system on my list, and I'm raking in millions pretty fast. I haven't gotten any more 2 million missions but now 300k to 1 million is pretty common.
Considering that I only need to travel and that speed is my strong point, I don't think that there are faster ways to make money. Although looting and selling Mk6 equipment might also work, if not as reliably.
Edit : =) I just got a mk6 antimatter drive from a korian invader... it's only 233M/s vs 220M/s for the plasma one, but it's a nice feeling to have the
best engine ^^