See HSEARCH-2674: it's approximately the same problem.
When you have multiple Hibernate Search nodes, all of them targeting the same indexes in a single Elasticsearch cluster, you may end up having some "dynamic shards" (i.e. ES indexes) ignored when querying, simply because each Hibernate Search node is only aware of the shards it created itself.

One solution would be to not ever mention the index names when querying (except when using explicit shard filtering), and only filter by type.
We'd have to check how well this performs, though: ideally Elasticsearch would first narrow down the list of indexes to query based on all the indexes that mention the targeted types in their metadata, but I'm not sure it does.