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I think I found the solution however it will require the tags to be stored in two separate fields (one to query and the other to aggregate on)

{
	"from" : 0,
	"size" : 0,
	"query" : {
		"bool" : {
			"must" : [{
					"term" : {
						"userid" : {
							"value" : 1
						}
					}
				}
			]
		}
	},
	"aggs" : {
		"suggest" : {
			"filter" : {
				"prefix" : {
					"tags" : {
						"value" : "win"
					}
				}
			},
			"aggs" : {
				"Tags_suggest" : {
					"terms" : {
						"field" : "tags_key",
						"size" : 20,
						"include" : {
							"pattern" : "win.*"
						}
					}
				}
			}
		}
	}
}

I can live with that, even though it will require twice the storage. And fingers crossed that ES wont remove aggregation filters in the future.

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