Hi Jorge,
In general, Identify is meant to provide feedback to user interaction, so works on visible layers in the map. So, if a layer is in the map and has identify capabilities (as defined on the service), it will be included in the IdentifyLayers operation.
You could discard the results for that specific layer from the identifyLayersAsync call (you get an array of IdentifyLayerResult objects back, each of which represents a layer), or you could identify only a subset of layers by calling identifyLayerAsync on each.
If you change the visibility, the user might notice that in the map view (but you might get away with it). Note that changing the layer opacity does not affect identify.
Hope that helps.
Nick.
