As a huge Zelda fan, I'd say the series still has a long way to go before it gets anywhere near Potter levels of popularity. Pokemon? Yeah. Mario? Probably. Zelda is not there yet. It's very much still the runt of the Big 3, ToTK or no. We'll see what the movie does for the franchise.
But in terms of health of the IP, I definitely think there is a case to be made there. There is no doubt Joelle's crusade has diminished the franchise's legacy a good bit, especially amongst younger audiences. It is still very popular and any new Harry Potter project is going to get a hefty amount of attention, full stop. But I think the Star Wars example is a good one, it's potentially a media juggernaut and has some impressive victories under its belt, but it's no longer at the point where a project is guaranteed to hit a massive home run like Pre-Endgame MCU or Pokemon are. Even throwing Dumbledore's name in the last film couldn't get people to watch. Zelda has been on a big upswing and is more popular now than it ever has been, I'm curious to see where it goes.