Hi jmsjms,
What do you mean by "The sharepoint see the schema of the sql database but cannot read the data", have you encountered any permission warning or something? Is there valid data in the specific tables that you were trying to retrieve from?
I don't think you need worry about Named pipes, it wont work with Azure SQL Database because named pipes is a network protocol optimized for local LAN traffic. All connections to SQL Azure are done using TCP/IP. As the sharepoiint has seen the schema,
so let's say your connection is ok.
Meanwhile it can be some sharepoint configuration problem. Here's a good link for your reference.
Office 365 SharePoint Online BCS with Azure SQL Server Database
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