I don’t think there are specific best practices for developing e-commerce apps with Mendix.

I would however adhere to the more general best practices available from the documentation:

https://docs.mendix.com/howto/general/dev-best-practices

https://docs.mendix.com/howto/extensibility/best-practices-javascript-actions

https://docs.mendix.com/howto/security/best-practices-security

https://docs.mendix.com/howto/general/community-best-practices-for-app-performance