The new cut creator is near identical to the last version - it just looks for more ROM types (run088 gave me a list 'cause he was having trouble with booting zipped games), and stops recommending that you embed the thumb paths in the CUTs (I changed a default option from "yes" to "no").
But if you've got all your CUTs in one folder and all your thumbs in another, then you need to embed the paths anyway, so there's no point in running this new version. And likewise, if you're embedding the paths then XBMC isn't going to cache the files regardless of which revision you run, so it may be that you don't "need" to upgrade that, either.
But XBMC upgrades aren't usually much of a chore (unless you want to have library mode and scrapers and all that stuff that I've never bothered to learn how to use).
Regarding emulator names, because of the folder structure I use with my shortcuts, I ended up using shortcuts to point to all the emulators as well as to the individual game ROMs. So I defined all their names there, and I (obviously) keep all the shortcuts between upgrades and just re-add them as a source if I ever lose my sources file.
However, XBMC can actually alter the embedded title of XBEs directly. Look up your game/emulator/app whatever in the Programs section (as opposed to the File Manager), press the white button over it, and select "edit XBE title" (as opposed to "rename", which does something completely different). Hey presto, the new name you set will be displayed both in XBMC and in all your other dashboards. Since this is editing the program's own XBE, this change won't be undone if you upgrade XBMC later.
Usually, unless upgrading from a very old build, you can keep the "UserData" folder (which contains 99% of your settings info). Though even if it turns out that some of the contents aren't compatible (eg the "databases" subfolder, which doesn't matter to non-scraper-using people anyways), it's very seldom that the "sources.xml" file (which contains, well, all your sources - where your programs/videos/music/etc are stored) can't be kept.