Yes, but it's a non-issue. Backup your iPad at home. Then update at the Apple Store. It will warn you that you'll lose your data since you are syncing with a different machine, but proceed anyway. Losing the data make no difference. Once the iOS update is complete, go back home and restore from the backup you made. Your apps and data will be restore, but are restored onto the new iOS firmware.
Technically, the same thing happens when you update at home on your own machine. iTunes backs up the iPad. It then wipes the data & installs the new firmware. Once the update is complete, it restores from the backup it made at the beginning. No matter where you update, the data is going to get wiped from the iPad for a brief period.