Unless explicitly enabling/disabling the enhanced lookup preference, Salesforce doesn't set any value to the enhanced lookup preference to a custom entity object. And if a custom entity object doesn't have a value to it, it is omitted when retrieving the custom entity object through metadata API. So you will not see the enableEnhancedLookup field in the retrieved object's metadata file by default.
On the other hand, when deploying a custom entity object, Salesforce explicitly sets a boolean value to the enhanced lookup preference even if the enableEnhancedLookup field is not specified in the deploying object's metadata file. It has the custom entity object have a value of the enhanced lookup preference. That's why you see the enableEnhancedLookup field in the object's metadata file when you retrieve it.