Does updating emClient wipe out customizations? Do I need to set up signatures, filters, etc again?
It shouldn’t change anything, but there might be some changes in your settings if you are upgrading from a much older version. Between any 8.1.x versions it is unlikely to be a problem.
Before upgrading, make a backup using Menu > Backup just in case.
You can also export your settings as a precaution using Menu > File > Export > Export settings to xml file.