Will it come off using something like a wallpaper scraper? Or at least enough so that you can sand the rest off. A solvent would help if you can find the right one. White spirit (paint brush cleaner) would be my first option, but you may have to try different ones until you find one that works. If the black goo is in patches, I would put a thick layer of kitchen roll on top and soak it in the solvent, then just leave it for an hour or so before scraping it off again. Repeat as necessary. Obviously do it in a well ventilated area.
Biological washing powder may help with removing the smell if it's ingrained in the wood.
Drying the hutches in strong sunlight will help to disinfect them - and it's ideal weather for it at the moment.
I would definitely paint the inside (as well as the outside) of the hutches to seal them once they are fully dry. Any leftover household paint is better than nothing.
Worst case - can you replace the affected floor, or cover it with another sheet of ply, once you've got as much goo off as you can?