Armed Merchant ships

[Flaxpants]

Last night I attacked a large merchant just off the spanish coast- as the weather conditions permitted, I thought I would save some torps and take it out with the deck gun. Very quickly I realised that the ship in question was firing back at me, fortunately I managed to deal with him before he caused me any serious damage.
Having not played the game long enough yet to have encountered many different types of merchant ships, I was wondering how many of them are likely to be equipped with guns? Are there certain types of ship that are more likely to be armed? It turned out that this ship was carrying military vehicles so perhaps it has something to do with it's cargo- or do particular types of merchant ships carry guns regardless?