Hi, owner of a Fractal Define R4 here. On the top of the case, the two fans on top are covered up so no dust will fall into the case, but no, there aren't any dust filters if you are going to place fans there.
Yes, it will of course make more noise, more fans=more noise. Also, the top is not that hard (not loose either) and will vibrate a little when fans are placed there, and that will produce some sound. Don't worry about that though, you will only hear it clearly if the fans are at full speed.