You can apply tags to the events or use the source field to identify which logs came from which files.
Example using tags:
filebeat.prospectors:
- paths:
- /path/to/log/type/A/*.log
tags: ["log_type_a"]
- paths:
- /path/to/log/type/B/*.json
tags: ["log_type_b", json]
Then over in your Logstash config you can use a condition to apply whatever processing you would like.
filters {
if "log_type_b" in [tags] {
// do something fun like grok
} // else if ...
}