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wow! Nice work. I've been trying to build an index of shopify stores. Did you search for all domains pointing to shopify's name servers?

I don't think that would work as many people also use Cloudflare etc.

You may try using BuiltWith which is a paid service:

It works fine. Just issue a HEAD request when you are unsure and rotate proxies a lot l. Takes a bit of infra but definitely possible.

I mean simply querying nameservers won't work.