Marcin,
1) ArcGIS Runtime is missing a lot of Smart Mapping capabilites available in the JavaScript API. Heatmap or clustering are examples of those. In my case, I render the data on the server side and use MapService for visualisation.
2) GraphicsOveralys are designed to store temporary data. But, that needs to be tested case by case when using huge amount of data. It might be better to use FeatureLayer (with on interaction change cache) on ArcGIS Server / ArcGIS Online
3) No suggestions at all.
Hope this helps,
Adam