Got reply from support. DO NOT FORMAT HDD!
Quick translation of message I got back from support:
Hi Anon, Thank you for contacting support. I'm sorry you are experiencing problems with your hard drive after system update. Nintendo is investigating matter and has said that it's not wise to format hard drive because that doesn't fix the problem. I'll get back to you once I got more infromation. Thank you for your patience. Could you still provide following information for Nintendo Japan: HDD manufacturer and model, Wii U serial number
So to help on issue email Nintendo complete error message, HDD manufacturer and model and Wii U serial number.