Patric: you are dead right that storing chain in the pointy end is not a great idea. On the other hand, having dirty, wet chain in the accommodation isn't a great idea, either. Yes, we did stow our chain in a watertight chain locker, right up forward on Badger. I do the same on Fantail, too, but salved my conscience by limiting myself to 25m of chain, backed up by loads of rope. If you are anchoring in fjord country, I guess you will often be in more than 5m of water and if, like me, you prefer to swing on chain rather than rope, I guess you'll want more than 25m.
Overall, I think most people reckon the convenience - not to say additional safety - of having as much chain as you want, easy of access in the bow, outweighs the drawbacks of pile-driving, going to windward in a sloppy sea. From having now sailed quite a few miles in Fantail, I reckon I could happily carry another 10m of chain in the bow.