If a tenancy agreement is not stamped, it is then not a legal document. The renting period, rent to be paid, rights and obligation of the landlord and the tenant maynot be legally binding in case a dispute be put for legal action.
For property tax, you just reported the total rental income, including rates or not, in your porperty tax return for tax purposes. Whether there is a legal binding document is not of IRD's concern. The key issue is on the rental income received. However, a stamped tenancy agreement will give a strong support to the rental income received if IRD is in doubt on it.