Whenever I start NBs, or when I run a module, I get warnings that some modules use deprecated APIs. Is that why XYZ doesn't work?

[org.netbeans.core.modules #2] Warning: the module org.netbeans.core uses org.openide.compat which is deprecated: The
   classes in this API are all deprecated and can be replaced by more modern APIs.
...

This sort of message just means that some modules are using org.openide.compat, which is deprecated stuff that many modules use. Probably the particular culprit is ExplorerPanel, which is what you typically use if you want to show a tree or other view of Nodes. It's deprecated, not because anything was particularly wrong with it, but because it was in the wrong package - it created an undesirable dependency from the Explorer API into the Window System API, which became more of an issue when these were split into separate jars. There is no simple replacement - what should happen is to create some kind of utility module that depends on both and includes it or its equivalent.

Even if you're seeing warnings about some other deprecated module, it doesn't mean that you need to be worried (of course, if you're the author of the module being warned, you should fix it). There is an ebb and flow to the development cycle - after a release, it's not uncommon for some things to be deprecated, and there is an inevitable delay before all modules that rely on the deprecated thing stop using it.