The aforesaid problem has been resolved by Tally Solutions in Tally ERP 9 Release 6.0.2
Release Notes
The HSN/SAC was not displayed in the printed invoice when it was recorded with:
o Stock items predefined with HSN/SAC.
o Sales/purchase ledgers predefined only with tax rate and not the HSN/SAC.
This issue is resolved. Now, if the HSN/SAC is not defined in the sales/purchase ledger, but is available in any of the masters linked to the transaction, the same will be printed in the invoice.