When the option isn't specified for an individual plugin, it checks the pipeline-level setting. When the pipeline-level setting is also not specified, you get this warning (not an error).
If you want to lock in the current behaviour for all plugins in a pipeline, add pipeline.ecs_compatibility: disabled to its definition in your config/pipelines.yml. If you want to do so globally, for all pipelines, add pipeline.ecs_compatibility: disabled to your config/logstash.yml.