The two COM antennas on the Skyhawk are one for each COM and the reason is, both can RX and TX on their own antenna without the danger of one COM sending the TX directly into the RX part of the other. One antenna for RX and the other for TX is simply, a joke ... your CFI got you on that one :-).
One VOR antenna may serve for two NAV by introducing a duplexer to the antenna cable, because it is RX only, so far correct. But, the reason not to fit two VOR antenna is pure laziness. There are quite some Skyhawks with two VOR antenna, mainly the ones first fitted for IFR use on ancient avionics when there were no sufficient duplexer available.