[test][prefix][databases] Cleanup empty fields in v2 databases

While they are optional, beat/beat.editor> ensures that
you do not get useless empty fields that may look
like something is missing hence remove them from
here to ensure testing goes well.
2 jobs for clean_v2_database in 16 minutes and 20 seconds (queued for 1 second)
Status Job ID Name Coverage
  Build
passed #222629
docker-build
build_linux_37

00:14:22

64.0%
passed #222628
intel macos
build_macos_intel_37

00:16:20

64.0%