Actually, it could cost merchants more but not because of Apple Pay per se. It's more due to routing debit cards over Visa/MC, since that tends to be more expensive in general. While some stores do try to run debit over networks other than Visa or MC when you use NFC (such as Safeway), it tends to produce PIN prompts and other UX issues for those using their phones to pay. Plus, it might cause more credit card use, which also costs them more (whereas their customer base might be more likely to use debit cards now).
The debit-as-a-side-effect component is one that I hadn't thought of, so thanks for adding that. The last time I used PIN-based debit was back when Aldi was that or cash-only, so it slipped my mind. Still, it seems the notion that "Apple is getting money directly from ___" idea keeps popping up on various forums and in person, almost cyclically.
I'm waiting to see the "we don't take Apple Card" instances that will inevitably pop up if someone breaks out the physical card.