It's not about having vast numbers of passengers, its about an InterCity railhead like Wakefield having the full service throughout the day
There's a difference between having a full service throughout the day and all of this worrying about one service a day at half two in the morning not stopping there.
Wakefield is incredibly well served by the trains that pass through it - on the ECML between Kings Cross and Leeds/ Edinburgh, there's only York and Newcastle and York that see that. Plenty of trains run non-stop through Peterborough, Doncaster, Durham etc. Yet there's all of this worry about one train a day that runs non-stop through the Wakefield area?
Odd, since I thought you were all in favour of the diversionary benefits of alternative routes? Since that needs regular driver training to keep their knowledge fresh, we either give one train a day the flexibility over the various chords and lines that see no regular passenger service or we have to run a whole HST ECS around the various routes between Doncaster and Leeds on a regular basis to tick a box? Not very environmentally friendly...
Plus there's the potential for engineering etc. Not every night, not every week, but Network Rail need some flexibility - much better to have a regular window every night than have to close the line during the daytime and inconveniencing lots of passengers. There's a trade off where it becomes more complicated/ costly to deal with occasional disruption (than to not have a service). *if* this one train a day did stop at Wakefield Westgate some time after two in the morning then you'd have to keep the station open for an extra couple of hours, you'd regularly have to deal with a Rail Replacement Bus from Doncaster to Wakefield and a Rail Replacement Bus from Wakefield to Doncaster... just not worth it for the numbers involved.
If it wasn't for the need to get an HST back up to Neville Hill so that it can run a morning duty from Harrogate/ Hull/ Lincoln to Kings Cross then there probably wouldn't be a 23:30 from London to Leeds. Other big cities seem to cope without such a late night service from London - I'm not sure what makes Wakefield so special? There's maybe an argument for better late night services from Leeds southbound, but that's a whole separate discussion - and conflating it with the need for an arrival after two in the morning from London doesn't really help that case.