How to hide certain items in a term reference field?
You can use the Entity reference module to achieve this goal.


Install Entity Reference module. 
Create a view of terms, with a display type of Entity Referance, and your filters/conditions 
Create a field of Entity Reference type. 
In field settings: Choose its target type is Taxonomy Term. 
In entity selection mode choose 'Views Filter by an entity referance view'. Choose the view you created above in 'View used to select entities'. 
Now save it.