If one were to ask an assembler or anyone having to troubleshoot to board level you will probably find that a random scattering costs needless time and aggravation and some sort of order is appreciated. Fortunately PCB design software makes it a very simple task to order them as they appear either on the board or in the schematic. I prefer the former because it drives me crazy having to hunt all over the board to find "C172" while squeezed into an installed piece of equipment (and usually in a cleanroom bunny suit), but some find it more sensible to order them at the schematic level. Either way, its a great tool and I really recommend taking advantage of it.
Before auto re-sequence
After auto re-sequence. Some cleanup is still needed to make everything look nice but the re-sequence only takes a minute.
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Reference Designator Assignment