Does spatial index make dataset work faster?
Are there any disadvantages in having it?
All datasets in my sde don't have a spatial index. I thought I should add it to make things faster
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Yes, spatial indexes makes the spatial query faster. Check this: http://desktop.arcgis.com/en/arcmap/10.3/manage-data/geodatabases/an-overview-of-spatial-indexes-in-the-geodatabase.htm