Waterproofing nail holes in a hardwood bathroom floor?
Without the ability to dry on both sides, your hardwood flooring will eventually warp and crack unless you completely seal the surface. 

You can use woods like Ipe and Teak in wet situations (and indeed, those are the woods traditionally used for ship decks) but I don't think Tasmanian Blackwood has the same resistance. There's at least one amazing bathroom designer here in Houston that built an Ipe shower floor... 



... but that's got the drain below a 'tray' made out of ipe that can be removed so that it can be cleaned, refinished and/or repaired easily. It's strips of Ipe with gaps between them that are then nailed to cross-pieces that sit in the sloped pan of the shower. I'm not totally clear from your posting, but from what I think you're looking for something like that for your entire bathroom? 

The only other alternative that I can think of for you is face-nailing the wood, and then sealing it completely with an epoxy polyurethane. However, this floor will be extremely slippery when wet.

But, in general, wood floors in bathrooms are a bad idea and are something that you should rethink.