Check for DiscountAmount

DiscountAmount is zero, taxamount is zero

Where are you seeing that data?  Order values for non-taxable amount would not necessarily translate directly to the invoice(s).  Prices could be overridden during invoicing, partial shipments, additional discounts... you won't find answers just looking at one line on a summary screen.  Look at the details of the order and invoice(s) to get the whole story.

In Sales Order > Sales order quote and history inquiry>Lookup customer view, add NonTaxableAmt and InvoiceAmt which are all from SO_SalesOrderHistoryHeader table, since we do drop ship, most of our order without tax and freight, so for most completed order, this two amount matched, 

SO totals and invoice totals don't always match, and differences do not necessarily represent "corrupted" data. If there was an error during the journal update it is possible the value written to the SO header is wrong, but that kind of thing is very rare.

You'll have to look at the invoice history compared with the order history, manually, in detail, to figure out why the amounts are different.

Thanks Kevin, this make sense, let me review everything in details to see if can find a clue, Sage tech support log on our system, couldn't find any clue, just suggest us use Library master to manually update this value in Sales order history table.

I'm surprised at that Sage tech recommendation.  Raw data edits would not be anywhere in my list of suggestions for this, unless direct evidence of corruption was found.

What really matters is invoice history.