You can provide the Estimate/Invoice Number or any other related fields by configuring the corresponding place holders in the Email template associated with the Email Alert.
Click on the Gear icon and select More Settings -> Email Templates and select Show Email Content for any notification of your choice. In the tool bar click on Insert Placeholders option and select the appropriate placeholders.
Alternatively, you could click on + Add New Email Template in the Email Template under Email Alerts.
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