Breeding stock can of course be shipped across on the normal ferries, the ferry companies have no problem with animals being transported as breeding stock.
Not to be confused with live exports which are being shipped across purely for the purpose of being slaughtered at their destination, which is what the demonstrations are about.
I would imagine that the main reason for shipping live animals for slaughter at their destination is to meet the demand for halal meat which has to be slaughtered as follows:
"The food must come from a supplier that uses halal practices. Specifically, the slaughter must be performed by a Muslim, who must precede the slaughter by invoking the name of Allah, most commonly by saying "Bismillah" ("In the name of Allah") and then three times Allah Huakbar. Then, the animal must be slaughtered with a sharp knife by cutting the throat, windpipe and the blood vessels in the neck (while the animal is conscious), causing the animal's death without cutting the spinal cord. Lastly, the blood from the veins must be drained. This final step is performed because blood can harbor harmful bacteria, and also to ensure that there are no blood clots, thus keeping the entire body safe and clean to be eaten."
Live exports have just resumed from Ireland to Libya using the cattle carrier Al Mahmoud.
http://www.change.org/en-GB/petitions/end-the-live-exports-of-farmed-animals-from-ireland