Do the albums mentioned below cover all soundtracks of the series Naruto and Naruto Shippuuden?
No. As an avid fan of the OST of Naruto and Naruto Shippuden, I can say that the soundtracks you mentioned don't cover all the BGM's in the anime. They only include tracks that are played regularly in stereotyped sequences. Like 'Will of Fire' is only played during flashback/sad sequences and 'Morning' is played all across filler episodes.

Having said that, there are indeed few BGM's which are not a part of the 3 collections you mentioned. Like the BGM from Naruto episodes 210-212 where Naruto and Todoroki are chasing to find Todoroki's brother and the Shinobazu hideout. The soundtrack played during those episodes is rarely repeated. So, it didn't make the cut into those volumes.