Seems common for Gen5+. I wonder if it's a problem with the pink coolant (Toyota super long life coolant). According to Aisin they're using carbon ceramic seals in the pumps, and the unitized seal isn't anything new if the manufacturer can handle a decent level of precision.
Aisin pump and carbon ceramic seal:
http://www.rockauto.com/catalog/moreinfo.php?pk=1872126
I'm more inclined to flush the system out with distilled water and switch over to Valvoline G-05 (with 50% distilled water) from the local NAPA store. I'd try another Aisin aftermarket pump with G-05, or just switch over to a Bosch pump that can handle low-silicated coolants like the G-05.
As far as wheel bearings go they should easily last 120-150K miles (~193-241K km). So 46K miles is too early. Maybe a lower cost part? Bearing seal/moisture/lubricant problems? Alignment? Ask the dealer to keep the old part next time and see who makes it. Koyo or NSK should be decent.