Having officers in the boarding party with the Linguist, Merchant & Navigator skills is important but even than i've found they don't always pick up on suspicious ships.
I've picked up the merchant ''Rio Iguazu'' under Argentinian flag heading North East in AM97. Clearly on course for an English port like Liverpool but when questioned their destination was said to be the port of Rotterdam. My officer with the Navigator skill unbelievably somehow agreed this appeared to be correct. The documents were checked, it was found not to be unusual to have HE shells and spare parts go to Rotterdam. Being that close to the Welsh coast i didn't buy it and contrary to all indications given i decided to sink the ship. I was wondering if the game was going to penalize me but was quickly reassured when the lifeboats where showing an English flag on the map.
My other unusual example was the merchant ''Monte Nuria'' under Portugese flag in AM56, so on approach to the straight between Northern Ireland & Scotland. Said to be heading to the port of Lisbon which did not make a lot of sense to me out there but was cleared as correct. I don't recall exactly the kind of cargo being carried but there was also nothing suspicious about it. Since he was taking a rather long detour to Lisbon i did not trust it and decided to sink the ship. Turns out this one too was actually an English freighter.
So maybe the game has those moments where you can't really find hard proof of irregularities and are ultimately left to go with your gut feeling ? Had i picked them up elsewhere i would probably have let them go.
I did appreciate having to worry about the consequences of my decision as i'm sure in real life there would have been situations where you couldn't be completely sure too
