The company I work for always include an identifier so we know definitively the objects we created.
As an NS partner you often find bundles and scripts from 3rd parties and internal users in a customer's account so it's good to have that clear view.
If it's a small project I tend to include all the objects for that specific project.
On bigger projects where several devs are working on it, we tend to pull in the script objects specific to our own responsibility and then generate a secondary "general" webstorm project with everything else in, such as tabs / forms / workflows / custom records etc.
In GIT we have an overarching project repository and then for each area we add in the specific webstorm project folders...but that's a whole different conversation.