Yes, vertical is usually preferable. In the presence of consistent currents and suspended sediment, we have seen instances where a horizontal conductivity cell is scoured by the abrasive effect of the flow. When scouring is particularly intense, the electrodes can be stripped of their electroplated platinum-black coating, driving the calibration toward fresher readings. Sedimentation (silting) in the cell also drives the readings fresh of correct.
Mounting the instrument vertically avoids abrasive flow and sediment build-up while allowing wave motions and Bernoulli pressures to flush the cell.
Note that some moored sensors (SBE 37-SIP, 37-SIP-IDO, 37-SMP, 37-SMP-IDO, 37-SMP-ODO, 37-IMP, 37-IMP-IDO, 37-IMP-ODO, HydroCAT, HydroCAT-EP) have a recommended orientation because of their u-shaped plumbing configuration. Refer to the instrument manual for details.