[@AbysmalDemon]
Okay, so pirates prey on weaker things, right? They like picking off people. The less people there are, the harder it is to grab a bunch of goodies and run off without facing much opposition.

This is why there would be caravan trains and the like in the old days. Merchants would travel in big groups so that all their security can focus on protecting all corners- rather than being stuck alone. So three merchants meet up with two more from another city, halfway down the route. Then they go to their final destination at a third city.

If a merchant fleet is too small, they might consider meeting up with another so that they can travel together. Another reason why they might travel together is if their warp drives are super expensive, and can wear out after so many uses. So, a single ship opens up a warp large enough for all ships to enter hyperspace- the rest of the ships save a bit of life on their expensive equipment, and they can take turns.

So, as your Merchant Fleet 1 enters a system to wait a short time for Merchant Fleet 2, a JAF Patrol Ship warps into the system.

Queue diplomacy.