I contacted FX about this, and just got the following reply:
Contracts for shows are different for standard SD channels and HD channels, therefore it is not guaranteed that if a channel airs a show on the regular SD channel they get automatic rights to the HD version. However we are in contract negotiations with the distributor for NCIS and hope to be able to bring this series to you soon in full HD glamour.
I guess we'll just have to wait for a while.