Neither Dragon nor Duncan have yet received the Sea Ceptor upgrade. Defender is first in line and is expected to rejoin the fleet, post-upgrade, later this year.
I believe the T45s are also receiving ongoing, iterative upgrades in relation to anti ballistic missile capability. I think I'm right in saying that Dragon was involved in related trials last year, so it may be that, in addition to being one of only two T45s available for deployment at reasonably short notice, she is also relatively well placed in relation to T45 ABM capability.
Also, as others have noted, Dragon has received the PIP upgrade whereas Duncan hasn't.