Given that it operated for roughly 200 years I would assume that the Dutch trading post in Nagasaki was a profitable venture. Was this the case, and if so just how profitable was it? From what I recall in a lecture, they averaged only one ship arriving every year, though that could be incorrect.
A ship a year may be an alright average over the entire period, but during the early years there could be as many as seven. Granted, this still doesn't sound like much, but bear in mind that the cargo going out of Japan (mostly silver, gold and, later, copper) was very low volume, high value. The cargo going in was mostly silk and other goods from China, also fairly dense. Precious metals were, in fact, the point of the Japan trade.
When trading with Asia Europe always had the problem that it didn't have goods near as valuable to trade for Asian goods. This meant that they had to use silver and gold to make up the difference. The Dutch East India Company (VOC) tried to solve this problem by making enough money trading within Asia to fund its operations there. Part of this solution was selling Chinese goods for Japanese silver.
While they never quite got this system (which has always seemed like a kind of mercantile perpetuum mobile to me) to work, they did ship millions of guilders worth of silver from Japan, with a peak of 7.4 mln in 1639.
EDIT: source is Israel's Dutch primacy in world trade
You're correct, it was only one ship a year. That was all the Tokugawa permitted. However, it was usually a massive carrack (Much like the Portugese Black Ships) carrying huge amounts of cargo. Cabbage, tomatoes, coffee, beer, tar, and large amounts of silver and other ores contributed to its profits.