EC card transactions in stores can be processed in two main ways. One as Electronic Cash (with your PIN) and one as Elektronisches Lastschriftverfahren, in which the store simply processes a normal Lastschrift using the BLZ and Konto-Nr. from the card. Like any Lastschrift, the bank account owner can have the charge reversed (though their legal liability to pay does not thereby vanish).
More info here:
http://www.zahlungsverkehrsfragen.de/kartenzahlung.html
Credit card acceptance is low in Germany largely, I think, because Germany very much has a cash culture. The credit card acceptance fees aren't really higher in Germany than elsewhere, but the consumer expectation that a store will accept credit cards and the credit card penetration rate are such that stores don't feel a need to offer such options. Accepting cash may well be cheaper, but it isn't free either--it costs money to count, safeguard (armored car services, etc.), deposit, etc.