Regarding passenger line mergers, I just put in reciprocal links between the affected lines, and don't even try to build a hierarchy among them.
Regarding ship name changes, what I do is link up from the sailing to the category for the ship (where all the sailings under a given name link up to a category for that name), but then link from the ship category to the free-space profile for that ship, which I always name according to the name at launch. The free-space profile also gives all the names (and owners) the ship sailed under, and connects to all the appropriate categories, so the free space profile becomes the main point of reference for each ship.
Regarding the genealogical value of doing this, I started out doing this just because I wanted to know which ships my assorted ancestors took to get here. (I have this fantasy of getting scale models of each ship, and displaying them in my living room.) But after I'd been researching for a while, I discovered that some family members ended up marrying people who had sailed on the same ship, so those passenger lists can be helpful in sourcing people. I have also seen a few cases where Royal Navy officers ended up marrying the daughters of more senior officers they served under. At least in the 18th and 19th centuries, the Royal Navy seems to have had way more family connections between officers than I ever imagined.