In email template is there a way to add custom data source from the script?

I think you'd have to gather up and store any details you want in one or more custom fields on the record you're emailing against, but interested to know if what you're asking is actually possible.

I have used a JSON from a custom field in Advanced PDF template, I am assuming this should work in Email template as well.

I know to do it in advance PDF but not in email template, its looks like i cant do addCustomDataSource

Would you mind trying populating a custom field, using it via ${customfield} ?

No, I am sending data in the mail that's not individual for a record or entity

you can use a beforeLoad script depending on the context

I just have to add data object to a email template with suitescript.

not an option, all method are based on setting fields on a record