I cannot absolutely answer the question, but in general, the purpose of fermentation in general and kefir specifically is to make the nutrients more bioavailable. In "Nourishing Traditions", Sally Fallon talks about how the kefir bacteria kill other, dangerous bacteria and break down casein, which is quite difficult to digest. Maybe someone else can more specifically answer the question about lectins.
I make my own water kefir. I was interested in low lectin or lectin free deit. I love my water kefir! Do I have to give it up? I really cannot find the answer anywhere! I drink about 10 to 12 oz a day.