Question:

Why are Picklist Values being inactivated by VPK package deployment in Vault?

Answer:

Picklist values are actually not allowed to be deleted in Vault. This is because they can be referenced by existing documents or objects records. Allowing their deletion causes issues where documents and object records have values that do not exist for fields. 
 
The normal functionality for VPK deployment is that object subcomponents are overwritten during the recreation process. However, this is different specifically for picklists because of this issue. Due to this, VPK package deployments inactivate picklist values instead of deleting them. 

Related Documentation:

Vault Help Documentation: MDL Overview