SPI Clock Frequency changes when level shifted
Make the frequency measurement on a scope.  It is probable that the waveform coming out of the level shifter is being misinterpreted by the meter.  It is possible that this is just due to the different voltage, but it could also be distorted or rounded off.  And a saelae logic analyzer may not provide enough information if the signal is distorted in some way, you will likely need an actual DSO with a decent analog bandwidth (bandwidth of 1/2 clock frequency is the absolute minimum required to get the state (1 vs 0) but not the shape, bandwidth of 10x clock frequency will give you a very good idea about the shape).