This isn't new.
When Nintendo first started digitial releases in 2011, their first offer was double the Club Nintendo coins to anyone who bought New SMB2 digitally, and last year they offered DK: Original Edition for VC exclusively to anyone who bought selected first-party games digitally. They want to encourage digital purchases, yes. So what. They're a business, they're supposed to promote stuff that is in their favor.
You just can't have your cake and eat it too. Pick whether it's more important to have Windwaker HD physically or to play it now, and support that. Be glad they're still offering you a choice.