Update:
Empty directories are symlinks in the original repos, RH tooling is not reflecting that in the final src.zip, entries whitelisted in the checks.

Empty java files come from upstream, whitelisted in 3.2 config for src zip checks:
ApplyImagePullSecretConfiguration - fixed in the latest version - https://github.com/dekorateio/dekorate/blob/3.7.0/core/src/main/java/io/dekorate/kubernetes/configurator/ApplyImagePullSecretConfiguration.java
ProjectParseResourceFileTest - https://github.com/dekorateio/dekorate/issues/1236
DirectoryAssetTestCase - https://github.com/shrinkwrap/shrinkwrap/issues/155
TCKVerificationSupport - https://github.com/reactive-streams/reactive-streams-jvm/issues/550
javaparser - files are intended for testing of incorrect inputs and file naming
BigObject - https://issues.redhat.com/browse/ISPN-15116

Original description details:

These directories are empty:
io.quarkus-quarkus-parent-3.1.2/extensions/kubernetes-service-binding/runtime/src/test/resources/k8s/test-k8s/.hidden-symlink-dir
plexus-utils-3.5.1/src/test/resources/symlinks/src/symDir
plexus-utils-3.5.1/src/test/resources/symlinks/src/symLinkToDirOnTheOutside
service-registry-2.4.3.Final.GA/docs/getting-started/assemblies/getting-started
service-registry-2.4.3.Final.GA/docs/getting-started/images/getting-started
service-registry-2.4.3.Final.GA/docs/getting-started/modules/getting-started

And there are 523 empty files in sources archive. Full list can be found in the attachment