If the wood has not rotted, and the bottom is open to the air which is sounds like it is, if you stop the leak, eventually, it will dry out. A dehumidifier in the basement and a fan blowing will help. If you can see the edge of the ply from where the toilet flange goes through the floor, you can poke at it. If it is soft and crumbles, you need to tear things up. If it is still solid, it will dry out. Something like an ice pick or scratch awl will help to determine if the wood is bad.
A dehumidifier in the bathroom and using the ventilation fan after a shower will help, too. While the grout joints aren't huge in area compared to the tile, they will wick moisture out that way, too. A porcelain tile (the more common one for floors these days), isn't porcelain if it has more than 0.5% moisture absorbtion - IOW, it's pretty impervious, but even it will let moisture out over time. Take something like a ball bat or a big screwdriver handle and tap on the tile. If they sound like they are hollow, you need a tearout as they've debonded. But, assuming you used thinset, it doesn't degrade in moisture. Only if the wood expanded enough to break the bond, or the floor is rotting, does it have to come out. Even if you've sealed the grout, moisture vapor will still escape (assuming it's not acrylic or epoxy).