I am developing a database which has data sourced from many different applications so, I use the schema name to differentiate the source application.Does it make sense from an organizational point of view to create objects in separate schemas?
Yes, that makes perfect sense.
Database schemas are “name spaces” for clustering objects that belong together, with the added benefit of schema permissions that allow you to deny access to all objects in a schema at a single spot.
From a security perspective, you should no only use different schemas, but also different database users to access the different applications. That way it is easy to deny an application user access to data belonging to a different application. Doing that, you can limit the loss if one of your applications is compromized, e.g. by SQL injection.