> Were they actually stopped?
I think the broad, practical answer to that is 'almost certainly'. I'm pretty sure if warships hadn't shown up and asked to come over and have a chat, the ship wouldn't still be sitting there. There's also probably a very technical legal answer which may indicate they weren't "stopped" at all based on the precise wording actually communicated and relevant maritime law.
Interestingly, a long time ago I got to experience being on a freighter in the South China Sea and having some sizable Singapore navy warships pull up and ask to have a chat and take a look around. Warships pulling up at sea certainly has a way of commanding your undivided attention. It's like being pulled over by a cop, except the cop is heavily armed commandos in an Apache attack helicopter.
I suspect the only reason the navy hasn't boarded that ship yet is because the captain is being ordered to stonewall by the owners and the government would prefer to avoid breaking maritime law (especially with everyone paying attention). However, if the relevant governments determine there's sufficient value in searching the ship, they'll just have their maritime lawyers come up with the best excuse or "exigent circumstances" pretense they can and board anyway.
The ship I was on was flying a Liberian flag but Indonesian owned. Given that we were in international waters and these guys weren't even customs, police or port authority (who are the dudes who usually pull over freighters), the captain could have technically denied their request but he didn't even consider it. He later told me, basically, if you are not 'the droids they're looking for' then you let them the fuck on board. As a commercial hauler there's simply no upside to making trouble for the Navy, they have a lot of ways to ruin your day and you might someday need their help if you've got an emergency (or pirates chasing you, which is not impossible in those waters). The only freighter captains who insist on exercising their rights under maritime law when facing a naval warship typically have a political motivation or maybe are actually pirates, spies or smugglers (of weapons or people - warships don't give a fuck about that undeclared container of stereos). Naval warships (at least in that area) also don't usually care much about expired paperwork, lapsed passports or even outstanding warrants. They aren't law enforcement and a warship like that costs over a million dollars a day to keep at sea. They are there under national command authority for reasons that are way above a freighter captain's pay grade. The captain and crew are usually just contractors hired to drive the ship. Our captain had been at sea 15 years and that was the first time he'd ever had a naval warship pay any attention to him.