Things that come to mind immediately are:
1) the presence on the enemy ship of an officer who has especially relevant information that might lead to another mission
2) the presence of hardware on board that we might need (like the daka generator)
3) the presence of a TSN traitor on board
4) with war coming, might the situation become so serious that capturing enemy ships could become a viable source of ships, or at least spare parts? Thinking back to the Napoleonic wars here (as Adele would), where captured ships also meant prize money. Not that we should go the prize money route, whatever the Pirate King might wish…
I’m sure there are more possibilities.