In your webconfig-model.xml, set a property showInQB for a <fieldconfig /> to true to hide a field from a Class.
An example of hiding an attribute field:
<class className="org.intermine.model.testmodel.Manager">
<fields>
<fieldconfig fieldExpr="age" showInQB="false"/>
</fields>
</class>
An example of hiding a Reference or a Collection field:
<class className="org.intermine.model.testmodel.Manager">
<fields>
<fieldconfig fieldExpr="address" showInQB="false"/>
</fields>
</class>