It depends on the molecule and the type of a chemical reaction. In simple chemical reactions molecules literally randomly collide with the probability proportional to their concentrations, which gives rise to the law of mass action.
However, in a cell, in addition to simple diffusion of the molecules, there are also means of directional transport of ...
You're reading too much into the authors statement.
The authors simply claim they have no evidence for any mutations in the working copies of the genes, and therefore not even preliminary evidence for a recessive mutation.
You're right that if they had found mutations in either gene, this wouldn't be sufficient evidence to conclude the translocation unmasks ...
RNAi can happen in the nucleus as well. This is better documented in C.elegans but there are some references supporting nuclear RNAi in mammalian cells too: