"I am wondering how much waste to plan for when winnowing cocoa beans into nibs so I can plan accordingly with the beans. How does this affect ordering pre-cracked and winnowed nibs from you? "
Very generally speaking, the husk accounts for about 20-25% of the mass of the cocoa bean.  So, if you have 1 lb of cocoa beans, you can expect to lose about 3-4 oz.  That's why if you order 1 lb of cocoa beans as nibs, you will receive about 12 oz of nibs.
Also, as it is related, you can expect a touch more husk in your raw nibs than roasted nibs as they simply do not winnow as well or as completely.   After you roast your raw nibs, you may find you wish to pick out or hand winnow a touch more.  That said, a touch of husk in your chocolate is not the end of the world, and you might be surprised just how much is in many commercial chocolates.  0.5% is the number I've often heard batted around.  If you weigh out 0.5% husk you will it looks like quite a bit - and quite a bit less than even what is left in raw nibs.
Happy Holidays every one.
We will be closed next week for a much needed break and family time.  If you REALLY need something, send me an e-mail and I'll do what I can to accommodate (as I always do), but otherwise, please don't expect any movement on your orders (I'll leave the stores open) until the following week.