The only risk of ordering online for in store pickup is it'll get cancelled. If the store doesn't have them, the store shouldn't show availability; and if the store does or should have them, but the employees "can't" find them or for whatever other reason, your order will get cancelled. When you place your order for in store pickup (don't forget 1% Ebates!), you'll receive an email with the subject, "We've received your order, but it's not quite ready," telling you to wait for another email notifying you your order is ready for pickup. Then, BB will send another email very quickly if your order is cancelled, or an email with the subject, "Your order is ready for pickup."
With all the PPDG/eBay specials recently, I've been redeeming a lot of BB GCs for Disney GCs by ordering online for delivery and in store pickup. (I prefer ordering on BB .com so I can use Ebates for 1% cash back compared to Shopkicks points that are worth 0.8/100 when redeemed for GCs. But then, time value of money). I ordered a bunch of Disney $50 GCs for delivery just about two weeks ago, and ordered another bunch of Disney $50 GCs for in store pickup two days ago (because $50s weren't available for delivery). Both orders went through without problems (I usually use only enough GCs to cover all but $5 or $10 that goes on my CC). I was also a little shocked that Disney $50 GCs weren't available for delivery, but seeing that $25s were, I think BB .com is just OOS on $50s. I'll be checking back occasionally.
P.S. I didn't notice anything different about my local BB store's GC selection. They still have Disney $25 and $50 GCs, restaurant, Netflix, iTunes, PSN, movie theater, gaming and gas cards, etc. No eBay (lol).