Should I use multiple beats input in Logstash?
So still not benchmarked much, but after a quick code inspection and a bunch of reading about netty and logstash in version 5 the input is not the bottleneck to worry about.

Logstash team did put a bunch of work in the way the filters and outputs plugins are run in parallel, the beats input plugin wait for a batch of events, and the performances problem have indeed been solved in version 3.1.0 by the rewrite I quoted in the question.