Hardwood flooring

We recently bought our house, which was built in 1932. The carpets on the stairs and 2nd floor were a mess so we pulled them up. Pine boards beneath. Very rustic looking – they won’t be “perfect”, but we don’t need them to be. We like the look. There are a lot of nails though. They are pretty big and we couldn’t get many of them out so we sunk them in (maybe too far so the holes are even bigger), sanded as directed and are now ready to fill the holes then do a final sanding or NOT fill them and move right onto the polyurethane. What will happen if we don’t fill the nail holes? Will the polyurethane fill in the holes? Will it look OK or be cloudy? We don’t care if you can see the nails. We experimented by filling some nails holes in a section you can’t see and we can’t match the putty exactlly. It’s too noticeable – and detracts from the beauty of the floors. And – even though the nail holes are also noticeable we like the way that looks better. Thank you!