What are the consequences of omission or late stamping a document?

Both the landlord and tenant will be liable to civil proceedings by the Collector of Stamp Duty of the Inland Revenue Department when there is an omission to stamp the relevant document. Penalties will be imposed if the tenancy agreement is not stamped before or within the time for stamping, by the Collector of the Land Registry, with a penalty, upon payment of the stamp duty. The amount of penalty will depend on the length of the delay.

Length of delayPenalty
Within 1 monthDouble the amount of stamp duty
Over 1 month but not exceeding 2 months4 times the amount of stamp duty
In any other case10 times the amount of stamp duty

One might apply for remission of penalty depending on the individual circumstances of each case, application form can be found in: https://www.ird.gov.hk/eng/pdf/irsd127.pdf

Indeed, getting your tenancy agreement stamped is very important. Only stamped tenancy agreements can be lodged with the Land Registry for registration. As the Court does not accept an unstamped tenancy agreement as evidence, the unstamped tenancy agreement would be unenforceable by the court in the cases of breaching of the tenancy agreement.

Reference:

Late Stamping and Omission to Stamp Document: https://www.gov.hk/en/residents/taxes/stamp/late_stamping.htm