I'm using 0.90.11 but I have seen this behaviour in older versions.

The total_shards_per_node setting is set via a mapping file living in 
$ES_HOME/config/templates/logstash.json.

The relevant part of the mapping is:

{
    "logstash" : {
        "template" : "logstash-*",
        "settings" : {
            "index" : {
                ...
                "routing" : { "allocation" : { "total_shards_per_node" : 2 
} }
            }
        },
        "mappings" : {
            ...
        }
    }
}

If you need any other information let me know. I still have the cluster in 
a yellow state. It also did the same thing this morning.

node01 - 2 (3)
node02 - (4)
node03 - (0) 1
node04 - (2) 3
node05 - 0 (1)
unassigned - 4

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