If you or someone you know has a supercapital and don't know the answer to this... please show up at Auga VIII - Moon 2 - Republic Fleet Assembly Plant... we will show you how to properly... store... your supercapital.
In all seriousness... Supercaps can use the "refitting service" that carriers (and the Orca and Rorqual) offer... however they cannot be stored in the ship maintenance array. Reason? They are simply too big. The same applies for storing supercapitals in supercapitals.
And to preempt your followup question... no, there is no way to package and transport a capital/supercapital ship into high-sec. Not even a freighter can do this (this is why freighters do not have any high/mid/low/rig slots). Reason? Capitals are not meant to be in high-sec.