There are a couple of reasons why an Account owner might not receive email alerts from a workflow or approval that is associated with a custom object.
Email alerts configured with 'Account Owner' as a recipient type will only fire if the custom object has a Master-Detail relationship with Account (with Account as the master). If the relationship is a Lookup only, the account is not treated as a parent record and the Account Owner will not receive the alert.
The email alert may not be received by the account owner in two scenarios:
Note: When changing table relationships and field types, please consult Help and Training to ensure that you maintain the desired data integrity.
For more details on when you can use the Account Owner in email alerts, please review Recipient Types for Email Alerts.
This is also in development as per this idea on the idea exchange.
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