There are a few reasons why some dogs bark on course. Some of them have been already mentioned. Shelties are very well known for barking on course lol, along with a couple of other breeds.
Barking can be a control issue as well, meaning the dog should learn to have more self control.
I think you have to determine whether the barking interfers with the success of the run. If the dog is barking AND spinning, that probably is late info from the handler, as the dog doesn't know where it is suppose to go and is letting the handler know it (in short telling them to smarten up lol).
If the dog is barking to the point it can't run without not looking at the handler and is missing directionals, dropping bars etc, then running courses should be stopped and retraining begins, imo.
It can also be a relationship issue between the dog and his/her handler. I know of one team, that the dog barks non stop and it even blocks the handler, getting in close, barking and not responding to directionals. When someone else runs the dog, no barking, no blocking and it runs nicely.
Barking at the handler is not faulted, but if the barking progresses until the dog is nipping and/or bitting the handler......that is faulted.
Last year at a small local agility trial, we watched as a woman came on course with her dog (looked to be an aussie mix). She puts the dog on the start line and leads out to the first jump, it starts barking at her, she releases it, it runs to her attacks her feet, she gets it to stop, gets it over the jump, dog continues to bark, then it attacks her feet again, she manages to get to the next obstacle, dog barking and attacking feet............the ENTIRE run was like that. This person trains with someone that I know, that trainer is well known for having novice dogs and handlers running full courses quickly, with little or no foundation skills etc. I have also seen many dogs from that trainer, have self control issues that appear as spinning, barking excessively and bitting the handler........go figure.
I saw that same handler this fall at the same trial, sitting in the stands watching others run.........she had given up.
Another one bits the dust, what a shame...............
Lynn