I've only bought non-agency ebooks from Kobo and have never been charged for sales tax. Amazon doesn't charge me sales tax on non-agency ebooks, either.
BooksOnBoard, B&N and Sony all have a business presence in my state, so I get charged sales tax on all purchases, agency and non-agency alike.
Strangely, they don't all charge the same tax rate. Amazon and Sony only charge the state portion, but B&N and BoB charge both state and local sales tax.
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