The performance of the information layer depends not on the number of the polygons only, but on the complexity of the polygons theirselves (number of the points yields a big influence). The performance issue was one of the major tasks we've addressed for the 2010.Q3 release. Could you, please, provide us with your KML so we could compare performance with new engine of the information layer?
The DynamicLayer can help. For the KML case you could preload all polygons from the KML and store them in the list. Then, when dynamic layer ask you for the items you can select polygons which correspond to the request parameters and pass them to the DynamicLayer.
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