Aren't you already acknowledging the receipt when you say thank you?

Thank you very much for your email.

Thank you very much for your email, the receipt of which I herewith confirm.

Or do you meant Inhalt (not Erhalt)

..., the contents of which I herewith confirm.

Doppelt gemoppelt. Man kann nur für eine E-Mail danken, wenn man sie auch erhalten hat, also reicht: Thank you for your e-mail.

we

Not sure here, but I think you can say:
Thank you for your email whose receipt we hereby confirm.

However strictly speaking, whose is referred to persons I guess, so it would boil down to something like:
Thank you for your email, the receipt of which we hereby confirm.

Anyway both sound unidiomatic to me, so I'd suggest to form two sentences... And on top of that—is an explicit confirmation necessary? Can't you just reply?