SQL Server 2016 Force Encryption Option
According to this StackOverflow post, if you have the server-level settings (referenced below) configured with ForceEncryption set to Yes, then that will enforce an encrypted connection regardless of the SSMS GUI Encrypt connection option being checked or not prior to making connections to that server. This may be a sufficient workaround for people where the "encrypted connection" is of more importance than the actual option being checked within the SSMS GUI.



According to Enable Encrypted Connections to the Database Engine (SQL Server Configuration Manager), you do this as such:


  To configure the server to accept encrypted connections
  
  
  In SQL Server Configuration Manager, expand SQL Server Network Configuration, right-click Protocols for , and then
  select Properties.
  In the Protocols for Properties dialog box, on the Certificate tab, select the desired certificate from the drop down for
  the Certificate box, and then click OK.
  On the Flags tab, in the ForceEncryption box, select Yes, and then click OK to close the dialog box.
  Restart the SQL Server service.
  
  
  To configure the client to request encrypted connections
  
  
  Copy either the original certificate or the exported certificate file to the client computer.
  On the client computer, use the Certificates snap-in to install either the root certificate or the exported certificate file.
  In the console pane, right-click SQL Server Native Client Configuration, and then click Properties.
  On the Flags page, in the Force protocol encryption box, click Yes.
  
  
  source