I checked the latest implementation of NIOFSDirectory in the lucene.net repository, and it is doing horrible things there.
In particular, it is supposed to be non blocking, but it is calling this method:

Inline image 1

This is now a SINGLE GLOBAL LOCK for all reads. 
So if you are trying to switch from the SimpleFSDirectory lock per file to a global lock across all indexes.that would kill any hope of good performance.

A proper way to handle this, at least on Win32, is shown here:

https://github.com/ayende/ravendb/blob/7c0cce5b1ab08f824d6c51908d88d00a417f5c1f/Raven.Database/Indexing/LuceneCodecDirectory.cs#L129

 

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