The issue here I think is that the through trains have been running from Kings Cross since at least 1982, and probably a lot longer. Thus they are a long term service and withdrawing them would mean losing a through service which has run for many years. I'd have guessed there is significant demand from London to Dundee, Aberdeen etc for at least a few trains a day, e.g. one in the morning, one around midday and one late afternoon.
I don't think there's such a need for Cross-Country to go up that way (not sure if they still do, have lost track) but from London it makes sense to me.
King's Cross to Aberdeen as a day train as existed since the 1960s, before that it was through coaches. A second day train was added in 1973, and both became HSTs in May 1979.
Inverness was served by a day train from Euston from 1974 (The Clansman), HST from King's Cross since 1984 (The Highland Chieftain).
Perth has been served variously by day trains from Euston in the 1950s & 1960s, extensions of the Talisman/Fair Maid from Edinburgh in the 1950s, and briefly by HST 1982-84 until that was extended to/from Inverness.
Various marginal time extensions were tries throughout the 1980s, you had at one point 5 London KX/Aberdeen HSTs, 2 Glasgow QS-London KX HSTs, a Dundee-King's Cross HST, a Taunto-Inverness-Paignton/Plymouth extension of a Glasgow XC train, Dundee/Penzance extended both ways off the Edinburgh-Penzance and running down from Dundee as a morning peak stopper into Edinburgh and the reverse back the evening.
You had a Birmingham-Glasgow extended to Aberdeen, returning the other way to Euston via Birmingham.
Etc etc
All these marginal time services were run because simply the trains were spare and would have simply cluttered up the depots, as it was all these services enabled additional services over internal routes and enabled the internal allocated stock to be freed up for other services.
At one point this system was so advanced that not one of the two-hourly Edinburgh/Aberdeen services was provided by internal ScotRail stock they were all either HSTs or inter-regional LHCS. ScotRail and BR knew how to squeeze assets!