Will hermaphrodite plants show male or female results when using the FemINDICAtor gender detection qPCR assay?

The results will show female, or no amplification on the FAM channel.

The hermaphrodite cannabis plant process does not synthesize a Y chromosome, it just activates sex determining genes elsewhere. The FemINDICAtor primers and probe target the Y chromosome and thus will not hit or amplify a hermaphrodite.