Molecularly, Nissl bodies are the densely clustered ribosomes on the ER. The basophilia is due to the RNA in the ribosomes. The question you have raised is a very significant one. For perspective, I quote a book Fundamental Neuroscience, 2002 (2002 is pretty old for neuroscience!)
The hillock is a region where materials either are committed to the axon (cytoskeletal elements, synaptic vesicle precursors, mitochondria, etc.) or are excluded from the axon (RER and free polysomes, dendritic microtubule-associated proteins). The molecular basis for this sorting is not understood. Cytoplasm in the axon hillock does not appear to contain a physical "sizing" barrier (like a filter) because large organelles such as mitochondria readily enter the axon, whereas only a small number of essentially excluded structures such as polysomes are occasionally seen only in the initial segment of the axon and not in the axon proper.
But a recent paper GG Farias et al. 2015, proposed the presence of a special area in the axon hillock known as the Pre Axonal Exclusion Zone (PAEZ) that tries to explain this polarized sorting by differential binding of microtubule motors.
Although the paper mainly talks of the sorting of axonal and somatodendritic vesicles as seen in the picture, they also seem to apply for the RER which actually are the basis for Nissl's granules.
This structure excludes not only somatodendritic vesicles but also larger organelles, such as the Golgi complex and the rough ER, in effect constituting the cytoplasmic boundary for the somatodendritic and axonal domains..... The exclusion of the rough ER and Golgi complex, in addition to somatodendritic vesicles, at the PAEZ suggests that a common restriction mechanism may operate for all of these organelles.
Well, as you might have understood by now, it's not a matter of the size of the axon/ dendrite since same sized vesicles are being diverted in either direction and as previously mentioned, even mitochondria enter the axon.