As Fred mentioned, there are always demos and loaners out there, and inevitably something that gets minor damage in shipping. Also consider companies like Amazon with liberal return policies - a "refurb" could simply mean a factory reinspection of a returned item that can no longer be sold as new.
It's also not like B&H says they have hundreds in stock, just simply that they have refurbs. Could be 5, could be 20. Either way it's likely not a lot, and definitely no cause for alarm in any way, shape or form. Shipping companies are likely far more responsible for what got shipped back than any QC fantasy issues. Nikon restored a camera to "as new" condition, so why not sell it? No one should be jumping all of any supposed "deal" given that one unexpected repair 9 months down the road could likely eat your savings, but at the same time it gives someone an opportunity to save some bucks. People buy grey market to do the same. Look at any Nikon product and you'll likely find that refurbs start popping up about 4 months down the road for all the reasons I mention.