BLDC encoder resolution too high?
Not if you are doing 6 step commutation. The extra transitions do nothing in that case since it has no use for the extra transitions.
Not to mention more pulses limits the maximum speed since the controller has a maximum rate at which encoder pulses can be handled. A 32,000 pulse encoder on a 10,000RPM motor is a 5MHz pulse train. You don't want to send that down a long wire if you don't have to and it's less noise tolerant because you can't filter the edges since they need to be fast for such high frequency pulse train.
Measuring speed by measuring time between encoder counts is also more finicky for the same number of encoder counts when your resolution is higher. Just because very small perturbations in speed are picked up and extrapolated for the entire revolution. Of course, you can measure the time between more ticks when your resolution is higher to get around this.
Also, price can certainly be more for higher resolution. Optical encoders which actually need a more intricate disc when the resolution is higher definitely cost more. A disc with only 16 slots in it is a lot easier to make than one with a few thousand.