The nucleus has constant mass but is further composed of Quarks. The mistake is to think that the nucleus is some solid "ball" because that is how it behaive on our scale... kinda like holding up three tennis balls at a distance: they will look like one "ball" but get closer and you can see the structure.

In fact, 99% of the atom is "empty" but the nucleus has constant mass which is spread in thirds amongst the quarks.

"What the bleep do we know" was a high production introduction into Quantum Mechanics and it's mysteries. However, it had too many "kooks" spouting off channeling and other odd theories. I would have been happier if they had stuck to real science... that's weird enouh without having to invoke spirits! But I don't think they are related as you say. Thoughts are intangible while mass isn't. The fact that we don't know WHY mass exists doesn't prevent us from understanding how it behaives, how to create and manipulate it, etc. Thought on the other hand we have no idea where it comes from or how it's created. At this time, I feel thought and mass are unrelated as far as science is concerned.