What does the Customer is_active flag do?

This is a legacy field, derived from Mage_Eav and present as far back as v0.7.14800 (and perhaps earlier). As such, it by far predates the earliest version of EE.

Whether the value of this field is used or not is a matter of implementation (such as it is for the catalog_category entity). I base this assertion on the fact that the Mage_Eav module does not provide any use of it as a base behavior for EAV entities.