I'm very sorry to hear important documents are missing after you updated iOS and SmartOffice versions. Unfortunately, there's not too much I can do to help you find them.
Before we consider them lost, can you tell me if you made a backup of your device via iTunes or iCloud? I am not an expert in iPad, or iClound, or iTunes, but if the documents are no longer on your device, the only hope for recovery would be to look to a backup.
There is one other possibility. What version of SmartOffice you were running when you updated? If you were running the original version of SmartOffice, there may now be two versions of SmartOffice (SO and SO2) on your device. The documents may not have migrated from old to new and would still be accessable from the old app.
I would also be interested to know what version of iOS you were running when you updated.