Motivation letter for PhD application
You do not need to state in your motivation letter that your MS research is not connected to the topic of your desired PhD project: your application contains your CV that already says what your MS research was about, so the information will be redundant. It most likely would be read as a sign of humbleness - that can be OK, but it's better to show humility putting an effort in learning, then in moaning about your ignorance. 

In many countries students had no exposure to doing ANY kind of research at any level before starting their PhDs. So if anything, the fact that you have done some sort of research in any field gives you an advantage.

There is absolutely no reason why you should already be familiar with the PhD project: the reason why you choose a PhD is not because you already are an expert in that matter, but because you want to become such an expert. On this part of your question, please see this other Academia answer