A few development boards are sold below cost, as encouragement to try a new processor, and in these cases, the seller may impose limits such as 1 to 5 sales per customer. So beware of those : that would cause problems when you suddenly need 100. (This is probably a bigger problem with $1000 FPGA boards containing $2000 FPGAs...)
Arduinos definitely don't fall into that category, and I believe neither the Beaglebones nor the Raspberry Pi do. But if there's any doubt, talk with a sales rep from the company involved. And on the BeagleBone, see the link in Eugene's comment.
Another possible consideration is that using a standard board, unmodified, makes it a bit easier for someone else to copy your design and steal your market. If that's a consideration in your case, a custom board increases the barrier to doing so, but it can probably never be eliminated completely.
Eugene correctly points out that continuity of supply is a potential problem too : if possible, buy all you need plus a few spares when you move from prototype into production. With open-source boards like Arduinos and Beaglebones, archive the board design files : that way you can have more made by another supplier if the original supply dries up.