Hi,
With HikaShop 3.x the display options of custom fields have changed to be more fine grained.
So first, you need to make sure that the display settings of your custom fields are correct (you can save them once just to make sure that the settings are correct in the database).
Then, since the settings evolved, it also required changes in all the views displaying them.
Did you update the PDF invoice plugin as well ? If you didn't and only updated HikaShop, it's no wonder it doesn't work properly.
Also, if you have made an override of the PDF invoice file, you'll have to redo your PDF invoice override with the new version or you won't see the custom fields.
Updating to HikaShop 3.2.2 won't help with your problem.