According to http://medievaldogs.wikispaces.com/Medieval+Dog+Breeds:
While many of today's dog breeds can be traced back to the Middle Ages (and some even older), breeds as we know them today, carefully defined by physical appearance, did not exist in the Middle Ages and Renaissance. Instead, dogs were classified by function.
Based on this, it is possible that Enek does not belong to a definite dog breed at all and instead belongs to a breed from which today's breeds are derived. In the books, he is only ever referred to as a sheepdog, and this is consistent with medieval people classifying dogs by function.
As mentioned in the question, Enek shares some traits that could associate him with Border Collies. His fluffy tail, erect ears, fur thickness and coloring, and leg length are consistent with the Border Collie breed. Enek displays a high level of intelligence in volume 13 (though this could just be attributed to personification), and according to https://en.wikipedia.org/wiki/Border_Collie, the Border Collie "is widely considered to be the most intelligent dog breed".
On the other hand, Enek's physical characteristics could also belong to a Dutch Shepherd. All the physical traits still match. The problem is that Enek is a cartoon and thus his traits are too indistinct to make a definite match.
In conclusion, there isn't enough information available to definitively determine Enek's breed. He could be an ancestor of the Dutch Shepherd, Border Collie, or some other herding dog.