EMV is the half of the new system that gets the news coverage, but the other half, point-to-point encryption, is more important. The transaction gets encrypted in the credit card pad, and the merchant never sees the card information. So if you break into their network, there's nothing there to steal.
How does the merchant do settlement at the end of the day or representments without that information? Are you maybe thinking about tokenization, where the merchant is given a token by the processor to store in place of the card number? The token is then used for followup transactions.