I honestly think that axons should atleast be soft-separated from the grid system, as in it'd be a lot easier to interact with dense axons if they only became highlighted upon selecting a connected neuron. If you look at my creature, the brain code is very messy with a lot of overlapping axons. I ran into an issue where if I arranged the axons in a particular order (if an axon had to cross another axon at its synapse point) then I wouldn't be able to adjust the synapse strength of the axon. This shouldn't be a system where order matters.
Falling back on using functions and calculus again, you could probably use a function which describes the position of a signal along a given length of axon (linear interpolation my beloved) and calculate the time it takes for the signal to reach the next neuron (which would create support for either grid / gridless axons). You could then inspect along the length of said axon and it would basically render a 'slice' of this singular at a given point in the graph.
Most of the frametime stuff should just be rendering signals if the player happens to be looking in the general direction and zoomed in enough.
Once again: I'm not a neuroscientist and I'm guessing its not as easy as it sounds. I don't know any of the math involved in neurology so I would understand if simulation accuracy couldn't be maintained with simplified calculations.