To your first question, that is server-sided. Only the host matters. When a new game is started, the names of the planets become unique to that game, and can be renamed using the Notes window in the galaxy map, for instance. During that initial setup of the game, on the host sever, is when the altplanetnames are applied. So, for instance, you won't see those names taking effect until you start the game (the regular auto-generated names are shown in the lobby).
This means that you don't need any sort of syncing between clients and hosts on the altplanetnames.txt files, which is nice.
For renaming the individual ships themselves, that is not something that is supported at the moment, and I doubt it will be something that makes sense to add because 1) it will increase save file size if needed, and 2) it serves no real purpose, as you say, and there are already more purposeful enhancements queued up in the suggestions forum than can be actually implemented. This tends to mean that the "just for fun" sorts of enhancements that get added are either very quick (which this is not), or something for which there is a lot of support that a lot of people want to see (which this could be, in which case that would be how it would get implemented). I'm not down on the idea, but there are just so many good ideas out there that I have to pick the ones that will give the most impact, if that makes sense. My to-do list grows faster than it shrinks, and has been for months!
Hope that answers your questions!
