Category vs Tag vs Table

I have a site that will hold roughly 1000 posts/articles from an in-house magazine dealing with Australian naval history. The articles cover a range of subjects (such as Aviation, Intelligence, Ship Histories, Personal Histories and the like) and I’ve created categories to suit.

The names of ships in an article is very important for research and cross-referencing but there are a LOT of ships. And, how does one distinguish between a ship that is the focus of an article and a ship that is merely mentioned in passing?

I have uploaded about 300 articles so far. I’ve used the categories to identify the subject material, and I’ve created “tags” for the ship names (and other keywords). But tags dilute the significance of the ship covered by an article; e.g. if the article focuses on HMAS A, but also mentions HMAS B, C and D, then 4 ships are tagged but the relevance of the article to HMAS A is no greater than any of the other three ships. In addition, there’s no way to create a list of articles by ship name or to cross-reference articles to the ship name in other material.

So, I am pondering whether I should instead create categories for ships that are the focus of an article and use tags only for the names of the “passing reference” ships. This sounds good in theory but it could add, maybe, 300+ extra categories; and in many cases there might not be more than one article where that ship is the focus.

Perhaps I am going about it the wrong way; might it be that I need a table devoted to ship names and create a meta link between the post and the table (in much the same way as, say, product names, work in an ecommerce transaction).