And as we've established, the vernacular for the usage of "the" before ship names goes both ways. Some feel it should be used, others feel it shouldn't. There's no universal consensus. But clearly the makers of Trek changed their preferences somewhere along the line.
And it's not just Trek ship names. Is it Batman or the Batman? Different writers seem to have different preferences. Sometimes it seems that "the Batman" is used by people less familiar with him and "Batman" by those who know him personally. On the other hand, there was a whole animated series called The Batman
in which he was routinely referenced with the article -- and, symmetrically, his foe who's usually called the Joker was known simply as Joker.
Come to think of it, why is it "the Joker" and "the Riddler" and "the Penguin" but not "the Catwoman?"