do we know the reason why they changed her name?
To fit the Ayanami-Makinami trend, or at least that's the obvious answer. The question is why there needed to be a trend in the first place. I've heard a rather nice argument that it's going to end in the revelation that they all share a nature somehow (as in being three of the Adams) but more likely it's just Anno making yet another derpish naval history joke: Shikinami
(sister ships, by the way) were both late 20s ships that lasted until WWII and then both bought it (Ayanami
at Guadalcanal and Shikinami
I don't remember where - by a sub, if I remember the first time I read this over); Makinami
was built after the war had already started and got wiped out within a couple years of being launched.Shikinami
actually survived the longest, if memory serves; but I think the point is more that Makinami
was a newer model of destroyer - and thus Mari is a new model of Eva girl. I would say it's rather misogynistic but honestly it's so obviously a MONEY MONEY MONEY ploy that I can't even criticize it on any other grounds.