Headline: "When the Queen went to war: Amazing pictures on QE2 as it sailed to the Falklands"
I agree with you Henry, but the word "it" is used in the headline of your URL in order to clarify who is going to The Falklands, the Queen or the ship.
It is one of the exceptions and has to be learned. I have seen it in some comprehension exercises. In fact, many non-native English speakers are more likely to understand the use of male and female references than native speakers due to the construction of their own languages, for example, Spanish, Portuguese, French, Italian.
Ship as a feminin noun is a tradition and, of course, many people don't know or, maybe, don't follow it.