^^^
A couple of very straightforward ones are that lines are far more prone to being closed overnight for engineering work, leading to regular disruption and diversions (especially now that there are virtually no parcels, newspaper trains or mail trains that 'must' run to regular schedules).
Freight assets have to earn money 24 hours per day. If wagons and locomotives are only used at night one would need to have far more to shift the same amount of traffic.
Many terminals will not have night-time staffing and there may be environmental constraints about intrusive noise and / or lighting for nocturnal operation.
Many long distance transits take longer than 6 hours, hence have to be during the daytime at some point on their journey anyway.
A night-only freight railway would find it harder to attract staff, especially drivers.