If some do a part-time PhD in Germany and work as full time in a research institute? Will it count as negative to become a professor.
A PhD is a PhD... it doesn't matter how long it takes, or whether it is full or part-time, the qualification itself is unaffected.
Amount of research produced over a certain duration has got some importance though.
The crucial question is the reason for the PhD being part-time. If that reason would reflect badly on your perceived fit as an academic, then it might have a bearing (if it implies too many family commitments, or lack of motivation perhaps).
However the fact that your full-time work is, you say, in a research institute is great for you in this regard. Your full time work is directly related to one of the roles of an academic. As such this should have no negative bearing whatsoever on the path to becoming a professor.