Yes you can use BN gift cards to purchase apps. You will want to make sure to enter your gift card either online into your account or easier yet (if you are on the 1.4 release on the NookColor) you can enter the gift card directly so it will be charged prior to your credit card. You can do this on the NookColor from the Shop home page, under My Account, then My Gift Cards. You can then add gift cards and it will show the balance on your gift cards.
Unfortunately the resale market for BN gift cards isn’t great, but this is a good deal if you regularly shop there. Why? Because BN gift cards have been in short supply lately and because 16.5% off face value is better than you will get anywhere else. Keep in mind this company isn’t in the best financial health so I wouldn’t stockpile these for too long.