A few points here:
1.) The main reason this wasn't done historically was a combination of practicality and international law. Major navies were more concerned with following laws against seizing neutral cargo (which consisted of a large chunk of merchant shipping), while their rivals didn't have many vulnerable transports. A scenario in which a navy both has control over a seazone to safely board ships and bring them back to harbor (since they're always going to send off a distress call) and also enemy shipping present there to capture in the first place is extremely unusual (usually contested waters are hugely-dangerous, such as the Central Mediterranean or various sections of the Pacific).
2.) On occasion, ships were captured by hostile navies, but other than coal (which isn't really used in WWII for ships), actually acquiring cargo wasn't so much the point. On the one hand, raiding either ships or land bases for ammunition occurred on rare occasion in WWI, while in WWII the more common convention was putting prisoners onto a captured ship (which sometimes would be exchanged with the opposing navy) so you didn't have to store them on your own ship, or leave them overboard in lifeboats (which was the norm in more violent situations, and for the last few years of the war). "Honorable" conduct in naval warfare got a lot less common as the war progressed, and this stopped happening.
3.) Coal versus oil is not a minor difference. Capturing ships and moving coal is feasible, if difficult. Refueling off of a captured ship is not realistic by comparison, and refueling at sea was already a hugely-complicated affair for using dedicated oil tankers, let alone siphoning fuel out of a merchant ship.
4.) While ships did surrender, if someone was going to seize the ship then captains would be more likely to scuttle the ships than let them be captured. Not all ships could do this, but its worth keeping in mind (unfortunately merchant ships cover a massive range, so while its easy to just look at convoys as "Liberty Ships" even late WWII represents a huge range of civilian cargo ships, oil tankers, dedicated troop transports, and seized civilian craft like liners, barges, or fishing boats).
Tl;dr, its possible but the circumstances for it to happen are fairly-unusual and improbable, requiring someone to run shipping past hostile-controlled waters. Most historic examples of this were either troop transports or heavily-escorted convoys (i.e. Operation Pedestal), and technically represent contested waters rather than hostile-controlled ones.