RE: Upgrading from Crm 2016 to Dynamics 365 - Javascript
I do not think you must change ODATA and SOAP to Web API.. From the upgrade standpoint, they are still going to work, but, moving forward, you should start using Web API:
msdn.microsoft.com/.../mt608128.aspx
"While this service will continue to be available as-is for years to come, we are deprecating it with Microsoft Dynamics 365. The Organization Data service has always been limited to performing create, read, update, and delete operations and never supported the ability to call specialized messages used in the Organization service, so it could never reach parity with the functionality of the Organization service.. "