I think that the boat sellers are correct in what they say, in so far as they have indeed purchased goods in Germany and as such they are duty paid. The buyers, therefore, are not breaking any law as far as I can see.
However, as is my understanding, "international waters" does not constitute "EU". So as far as I can see, the whole "EU free trade" argument falls down, because they are not selling the goods in the EU, they are selling thm internationally, which might as well be the USA, Australia, Russia or Uganda. It doesn't matter. The point is, the boat is now selling goods in international waters and it could be argued that any customer travelling to the boat, purchasing goods and bringing them back to England, may equally be considered to be flying outside the EU, and therefore the normal restrictions on customs and duty goods (such as only 200 cigarettes) should apply.
It seems that the boats owners are in a sticky situation as they are not breaking any law, but prospective customers might be if they fail to pay, or indeed evade, customs and excise duties.