It's generally no difference if you apply global or local bonded contacts.
Global bonded connection will bond all surfaces in "contact". Local bonded connection will let you override the global (and component) connections and also let you select line & point selections.
Like Jon Dahlgren says, the definition of both a global and local bonded contact does not differ in behavior when placed between the same faces. It is likely that your bonded version of your model is the accurate representation of the overall design. When a bolted connection is made the objects behave as one. Their vibrational modes of a bolted connection (with preload) and a bonded connection should be very similar.
Now, if you are just using this connection as a force transmitter to the rest of the model to see if somewhere else fails you would absolutely want to bond this connection and see if other failures appear.