The name in Krita 5.0 is only changed in the database and in the preset itself (because the preset always has a name inside its own file, which is independent from the filename). Renaming creates a new version of the resource. When you export it to a bundle (maybe potentially in the future also just export?), it will have a nice, pretty filename inside of it based on the current filename (exceptions are brush tips, patterns and I think gradients, because we can’t really change their filenames, because some resources still depend on that, I think. But with those, if you know you have some resource that depends on it, it’s better to leave it alone anyway).
So basically, if you rename a resource, it will look renamed all over Krita, but it will still have a filename that suggests the old name. This is also the same reason you currently cannot create later a resource that has the previous name of that resource. For example if you create “Brush A” and then rename it to “Brush B”, and then try to create “Brush A” preset, then Krita will ask you if you want to overwrite “Brush B”, because the filename would clash/collide. That’s a current limitation. Maybe in the future it will be possible to define a different filename for it to work.
It’s often like that, you gain something, you lose something. I think it was worth it though, now it’s more universal and integrated, everything happens automatically, it’s nice to use it from the developer’s point of view as well (when they are not fixing all the new bugs, of course ).