If you're doing commodity runs, you dont have a lot of high value loot at a time, but you're consistently cashing out and staying on the same server to do it. If a commodity merchant was offering me an alliance i know that i can leave him to his business and make a ton while he carries on. way more than i would make from a one-time shakedown. If i sink him, hes just going to switch servers since he knows common sense wont hold water in this one. Ally with the guy however, and the income you'll receive will far outstrip the one time payout of their current haul. Alliances with any other person is a 50-50 on being worth it compared to sinking them because you dont know how long someone is going to be playing for and their loot might as well work for you, but a commodity merchant is in it for the long haul and we all know it, that's what makes them different.
My point is, allying with a commodity merchant is uniquely the best alliance scenario and will net you far more than sinking them. You might be against alliances, but a merchant who pays protection fees is an even better deal for all involved.
Since I have been reminded ever so politely to "keep historical accuracy out of it because nobody plays video games for historical accuracy", I'll just deflect to that as the counterweight against "pirates gonna pirate". Being a murder-hobo makes you the DnD equivalent of someone saying "im just playing my character" when Chaotic Neutral is more of a permit for selfishness rather than a mandate. My question at the heart of all this is: Why attack commodity merchants if they're non-hostile and offering an alliance?