In a piece reflecting on how best to lay out schematics, Hackaday notes that whilst there are naturally many different takes on this, the key issue is really knowing who you are targeting with the schematic.
It suggests that if your audience is trying to figure out the circuit logic, you should probably go functional, but if you are trying to debug a circuit, the pin-number layout can be more helpful; ultimately it suggests that a combination of both is the best approach.
It adds that whilst the logical flow of the circuit should always be the main driver in any schematic, this approach should still be maintained when mimicking the PCB layout, given that this is usually best for beginners or those debugging a non-working board who don’t have access to the PCB layout.
The issue of whether to use functional or numerical pin grouping was also debated, but Hackaday suggests that being able to have both in the same schematic via embedded hyperlinks would bring the best of both worlds.