Venturi meters generally indicate velocity based on the differential pressure in the pipe, therefore that pressure is not referenced to atmospheric, or gauge pressure, at all, so if you have a negative reading on a differential pressure gauge, flow is in the reverse direction from that intended. If you are measuring the difference in flow via two atmospherically referenced pressure gauges one upstream, one downstream, you could see "vacuum" readings that correspond with flow in the correct direction.
Depending on the precise shape of the venturi, it may have a more rapid reduction in size in one direction when compared to the other; most I have seen have a quicker reduction from pipe diameter upstream with a more gradual transition back to the original pipe diameter in the downstream direction, so it may or may not give equivalent readings for equivalent velocities in opposite directions, but I would not expect them to be equivalent without a calibration to specifically verify that supposition.
Independent events are seldomly independent.