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For WebSphere Commerce Master Catalog data model (logical model), each product can belong to one and only one parent category. Moreover, each category can belong to one and only one parent category. Basically the model is a tree.

In the database model (physical model), there really have no such limitation / restriction.

The Master Catalog Management tool (Accelerator) and also contract management are build based on the logical model. So if the logical model breaks, then you cannot no longer use catalog mangement tool to manage the master catalog. Contracts may also be broken.

Here is a link from WebSphere Commerce Info Center that shows how to configure Sales catalog tool to manage the master catalog.