Nick here from Shopify.
I'm wondering if you mean a pop-up that occurs on the website when someone goes onto your website initially or do you mean more of an email that is sent to a new customer if they sign up to your mailing list?
If you mean a pop-up there are a few different apps from the Shopify App Store you can look into which will be able to help you with this. You can see some of them below:
If you were referring more to sending an email greeting, your best bet would be to look into collecting customer emails and maybe an email marketing campaign. Shopify has a guide for collecting emails here and a great blog post from the Shopify content team here going into more detail on marketing campaigns here.
Let me know and looking forward to hearing from you.
All the best, Nick