That is taxes. It goes to the owner of whatever Land your estate is on... If estate is in someplace like Genesis or Omegaton West Habitat that don't have a real participant LA owner, it's never been determined if the fee goes in to loot pool, or more likely in to FPC's pocketbook.
Also, shopkeeper has a 10 pec decay cost for every sale, so you need to figure that in to your pricing strategy to make sure you are pricing things correctly. Also, like the shops, minimum markup is tt+1. One advantage shopkeepers do have over real shops is that you can sell deeds there, but can't in shops since you can't drop deeds on an estate, which is an action that's needed to sell deeds in a real shop. Also, shopkeeper can hold stuff below 1 pec in value, which shops can't because of that silly rule that MA threw in that keeps people from dropping things below 1 pec value... so if you want to sell sweat stacks below 1k in size, shopkeepers are one ways to do it.