You're right that the input current is a minimum but there will be a high current flowing in the series loop (sloshing from L to C and back again). This could, I think, cause a lot more coupling.Don't forget there is both series and parallel resonance. With parallel resonance, current is at minimum.
If the antenna are not matched to each other it is easy to calibrate this out - by measuring the outputs of the two antennae in the same place and comparing them. Actually, tuning two antenna to the exact same frequency would be difficult - pretty knife edge adjustment aamof. A flatter response could be easier to deal with.
It is normal to make measurements using a 'probe' with very little coupling, so as not to disturb the system.