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At the risk of going over old ground, when the mission task became "Carrier Strike" not Air Defence, Fleet or otherwise, the SHAR was chopped. It would clearly have been desirable to run on both Harrier platforms but money was not available for SHAR improvements and the upgrades of the GR's within the JFH Fleet.
So we ended up with a Harrier GR9 Fleet that reflected the Defence requirements of a few short years ago but after a further cost driven review and despite the funds spent, chopped it and in doing so also removed the UK's Carrier Strike capability until later in the decade (ish). The Carrier Strike requirement remains but we thought we could get by without for the time being.
If HMG had then cut back on our involvement overseas we might not be having a debate over the non-availability of the Harrier and its ability to operate from our current carrier as and when needed.