You could try patching the holes and having the wood stained to match the rest of the floor

I concur, a flooring company can match the old wood floor plank and species. Patch and interlace new wood, sand and refinish to make it look as if there were never any furnace holes to begin with. Stay away from Lowes and HD.

Or get decorative registers that fit the hole.

Each hole is a significant job to try and match. Very hard to match stain without being noticeable.

Would be better off fixing the holes next time the floor is completely redone.

You could also get wood floor registers of a similar species wood and stain them to match the wood. It wouldn't be a perfect match but if they are close they won't be obvious. You could probably do a test stain on the back of the register to find the closest match.

how about those in the walls and ceiling?

Pictures of the areas would help

Get some pretty register covers like these: