While the keto server is running If I type in a new namespace in keto.yml sever does hot-reloads but In our project, each new customer gets a new namespace So each time a new customer gets onboarded is there any way programmatically we can add a new namespace.

there is no config API, but as you said you can (programmatically) update the config file and it gets reloaded not sure what you want to achieve in the end, but consider that namespaces are not isolated* if you are looking for multi-tenancy, have a look at https://www.ory.sh/docs/kratos/guides/multi-tenancy-multitenant or the #ory-network

I am able to Manually update namespace, Is there a way update namespaces in keto?