Even with an organizational subscription, you can still only add 1000 features directly to the map. When you add SHP or CSV directly to a web map, those features are stored inside the web map (coordinate and attributes). The more features you try to store in a web map, the larger it gets. It takes longer to open a web map because you could be transferring up to 10mb of data across the wire. These features stored in the web map are then drawn by the client application (web browser, mobile app). And the clients can only handle drawing so many graphics.
The solution to this is not to try to add SHP and CSV directly to a web map, but instead to create a web service out of them. With your organizational subscription, you�??ll create a hosted service in ArcGIS Online. By creating a service, the web map doesn�??t have to store all the features, it just references the service and thus, the web map stays small.
In the case of a map service, the client doesn�??t have to draw the features either, the map service returns an image to the client and the client displays it. In the case of a feature service, the limit is still 1000 features because of performance reasons. You are sending a request to the server to retrieve the coordinates and attributes for all features. This can be a large amount of data. Also, just like shapefiles that are stored in the map, the features of a feature service are drawn by the client. So, when you create a feature service, it's very important to set the appropriate scale dependencies. This is not currently exposed on the item details page, but will be at our next update.
Hope this helps,
Mike
