The rejoicing was definitely not universal. It really felt like the NeXT folks wanted to throw out pretty much the entire Mac (except keeps its customer base and apps) and any compatibility had to be fought for through customer complaints.
Personally, MacOS X bundles (directories that were opaque in the Finder) seemed like a decent enough replacement for resource forks. The problem was that lots of NeXT-derived utilities munged old Mac files by being ignorant of resource forks and that was not ok.
The 9->X trapeze act was a colossal success, but in retrospect it was brutally risky. I can't think of a successful precedent involving popular tech. The closest parallel is OS/2, which was a flop for the ages.
A large amount of transition code was written in those years. One well-placed design failure could have cratered the whole project. Considering that the Classic environment was a good-enough catch-all solution, I would have also erred on the side of retiring things that were redundant in NeXT-land.
Resource forks were one of the best victims, 1% functionality and 99% technical debt. The one I mourned for was the Code Fragment Manager. It was one of Apple's best OS9 designs and was massively superior to Mach-O (and even more so wrt other unices.) Alas, it didn't bring enough value to justify the porting work, let alone the opportunity cost and risk delta.
MacOS X bundles are actually NeXTStep bundles, and are behind the same idea in Java JAR files with META-INF directory, and .NET resources, due to Objective-C's legacy on all those systems.
Personally, MacOS X bundles (directories that were opaque in the Finder) seemed like a decent enough replacement for resource forks. The problem was that lots of NeXT-derived utilities munged old Mac files by being ignorant of resource forks and that was not ok.