If you de-activate an Item/Customer/Vendor then it can no longer be added to a module (Sales Order, Invoice, Purchase Order, etc.). However, it will still remain in the system and can be re-activated. Any modules already created with that Item/Customer/Vendor will remain unaffected and can continue to be processed.
De-activating a user will prevent them from logging into the system. Re-activating it will allow them to log in again. For departing team members it is recommended to either de-activate or delete their user and create a new user for new team members who are joining.