I agree on comment, when ever you set few special things like over writing characteristic or values it populates few extra filed, but the instances of characteristic will not be created, if a same characteristic is used in many places it will increase total table entries in different tables, but instance of characteristic will always be same.
You can co relate it for example material master, if a same material is used in many different BOM's , its entries in BOM component table swill be increased , but if you create new materials a table entries in Material master table's will be increased. so using same characteristic's will help reducing data base space. It will also help you reducing characteristic maintenance too.
refer below link to see various table used in settings up variant configuration in system.
http://scn.sap.com/docs/DOC-46807
Also check below thread to see linking of VC data.
http://scn.sap.com/docs/DOC-56688
Hope it may help you finding information you are looking for.
Thanks
Ritesh