Reduce the frequency of Supply missions so this doesn't happen: https://i.imgur.com/PCR3FYm.png
I'm not sure what the problem is that you are trying to point out in the image?
Are you frustrated that you were able to raid so many supply runs that you got so much cash? I'd have no problem with that kind of bank roll. The conqueror ain't cheap.
However, if it really bothers you, feel free to ignore the supply missions then. That is what I have done for much of my current campaign. I have two enemy bases available. A trader base near my HQ, and a Merc base in Antarctica. Most of the Trader supply missions have been at night, so I've freeing ignored them. Merc Supply missions? yeah, no thanks.
I do intend to farm the Trader base for some Guild masters, and may hit some more supply runs. But the last supply ship I went after had the Bonny facing 6 enemy right out the door. The only one with a Nuc was a Body Guard, looking right at me. My knees were rubbery as I anticipated it wiping out my crew. Fortunately I was able to coax a missed shot out of the nuke wielder with my Flappy Parrot. Lots of smoke and some Seductresses helped with the other issues. But generally, farming supply ships in Piratez is a far sight different than in vanilla.