I'll suggest that if the shipping company "prefers the wheels" enough to either reduce the shipping cost for caster equipped cases, or require the cases be equipped with casters to take the shipment, then leave the wheels on.
Admittedly, the truck drivers (and dock warehousemen) may "prefer the wheels", but to what benefit of the shipper or receiver? I have shipped and received a few cases (and speaker cabinets) that were caster equipped, only to discover that some of these caster equipped cases were free-ranging in the back of a cargo trailer for some or possibly all of the journey (and that was pretty ugly).
If shipping a >500lb board in a case (for example)... yes, having the case caster equipped will likely be a big plus. And chances are if said board in the case (on casters) is left to free-range in the back of a cargo trailer... it will only free-range till it likely soon-on does a face-plant.