I just checked ITA Matrix.
ANA does not charge YQ for Y tickets HKG-NRT.
Here is the fare construction for a random Y ticket in Oct.(the important part is in bold):
HKG NH TYO 596.55URFJ0O NUC 596.55 END ROE 7.79469 XT 90G3 120HK 45I5
HKG depart. tax is 90 HKD,
HKG construction fee 120 HKD
HKG security Charge 45 HKD.