@Bigivel:
You're talking of the previously reported only 3 episodes Breed arc! As you can see after the first filler episode the ratings decreased a lot and after it ended they grew again! Try to look at the ratings of >5 filler episode arcs!
First off, the ratings are higher in the filler arc. Ranking matters more than %.
Let's look at Post-Enies compared to Ice Hunter, compared to Thriller Bark.
322 - Canon (7.3, Rank 8)
323 - Canon (8.4, Rank 5)
324 - Canon (9.9, Rank 6)
325 - Canon (8.8, Rank 6)
326 - Filler (8.3, Rank 3)
327 - Filler (8,7, Rank 4)
328 - Filler (6.5, Rank 8)
329 - Filler (7.0, Rank 6)
330 - Filler (8.2, Rank 5)
331 - Filler (8.5, Rank 6)
332 - Filler (9.1, Rank 4)
333 - Filler (7.3, Rank 7)
334 - Filler (7.5, Rank 6)
335 - Filler (9.8, Rank 4)
336 - Filler (8.9, Rank 5)
337 - Canon (6.5, Rank 4)
338 - Canon (7.9, Rank 6)
339 - Canon (8.8, Rank 7)
340 - Canon (7.8, Rank 7)
Ratings fluctuate no matter what material is being adapted. It isn't a factor.
–- Update From New Post Merge ---
@Bigivel:
One Piece has around 7 episodes in production in advance, Naruto I don't know but let's assume it is the same.
The manga already ended 5 weeks ago and the public announcement of its ending was made 3 weeks before that. So they had the info at least 8 weeks ago, probably earlier giving that they talk directly to Shueisha, Kishimoto and his editor. The excuse of still in production doesn't really exist anymore!
Also what do you think of their Filler at the beginning of 2015?
The average production schedule for an anime episode is 3-6 months. Content that has already been planned and budgeted is not going to be changed due to the manga ending.
If they're still doing this halfway into 2015, then the scenario you're describing is a possibility (and doesn't really matter… as it's a money maker and the content they produce is more interesting than the manga itself anyways).