What effect does a journal having multiple ISSN codes have on reporting citations?
From what I can understand, currently active journals that are published both online and in print will have both a p-ISSN and an e-ISSN. This means that your paper (which will be published in both channels) will be attached to both ISSNs. See Wikipedia:


  When a serial with the same content is published in more than one media type, a different ISSN is assigned to each media type. For example, many serials are published both in print and electronic media. The ISSN system refers to these types as print ISSN (p-ISSN) and electronic ISSN (e-ISSN), respectively.[citation needed] Conversely, as defined in ISO 3297:2007, every serial in the ISSN system is also assigned a linking ISSN (ISSN-L), typically the same as the ISSN assigned to the serial in its first published medium, which links together all ISSNs assigned to the serial in every medium.[4]


ISSNs of different types for the same journal are connected through ISSN linking (ISSN-L). A file of ISSN links can also be downloaded from the ISSN website, to check whether specific ISSNs are really linked. You can also read about ISSN linking at wikipedia: Wikipedia: International Standard Serial Number#Linking_ISSN.