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.