Not my graphic - but the black ships are the amphibious ones - in other words LPD or LSD(A). It appears that grey ones are the ones we would expect to be assigned as and when. I think the shading differentiates between types of ship, such the two Type 45 destroyers in dark grey and two Type 23 frigates in the Carrier Strike Group section.
All the ships shown are in service. The vessel outlined with the legend of 'Additional Logistic Vessels' looks like one of the RO-RO vessels operated on behalf of the MOD. As no amphibious assets have been cut since 2010, and the RN as fiercely resisted attempts to reduce the capability (which started to wither on the vine during the years when Afghanistan was the main defence effort), I fail to understand the claim of cuts to amphibious capabilities.