NCSX is the worst for that stuff. If they ever even receive the bonus items, they hoard them to re-sell later. I've had good luck with Play-Asia and pre-order bonuses.
I've actually had no problems with them in the past. All preorder bonuses for games like Yakuza and other games arrived with the bonuses just fine. But it seems like their distributors have been sucking lately, particularly for stuff released in the past 6 months. I've resorted to AmiAmi these days since the prices at NCS have also gone up.
Yeah, I've seen them too.
http://www.ncsxshop.com/cgi-bin/shop/SGA-EOES.html is another example. Both say the same thing about surplus stock. Guess places got extra pre-order bonus stock, and instead of just giving them with copies bought on or after release, they decided to sell them for extra money.
Not for all items. when they shipped WKC without the bonus CD to me once, I inquired and they later shipped one to me when they got more shipments in. I inquired about the Ni no Kuni bonus and it seems that's not possible. I bet they'll be selling those soon since the game basically bombed in Japan.