Hmm... not exactly, but I am not sure I follow.
As I said, if you use NCAP_AFC(output), the capacity will be the nominal max. output capacity, like with power plants. So, in that case the capacity does NOT represent the max. amount that can be stored.
If your flow unit is PJ, maybe you should consider defining a SEASON level storage, having both input and output INFLOW with PRC_RESID = 10 (PJ), PRC_CAPACT=1, NCAP_AF(UP)=0.9 and NCAP_AF(LO)=0.2, and some storage efficiency/loss. That would be your seasonal storage part. If you create an ANNUAL level process producing INFLOW, you can define the seasonal hydro INFLOW distribution with COM_FR(INFLOW).
Then you could add a DAYNITE level storage hydro power plant consuming INFLOW (=input) and producing electricity (=output). For this DAYNITE storage you could use NCAP_AFC(output) = X, in order to define the capacity in terms of MW/GW, and the availability and capacity costs accordingly. And, as I already mentioned, the daynite storage capacity can then be defined by using NCAP_AFC(ACTGRP).