A lot of the issues are not HST related - there is a general lack of train crew cover just now (particularly Drivers), which means if crew don't want to work rest days, then there's the potential for cancellations right there. Factor in lieu leave, holidays, sickness etc as well
This is something of a systematic failure in the way the railways (and Britain in general) are run, I think - the reliance on staff volunteering for extra shifts to cover core operations. There are a multitude of reasons why it's done this way, of course, but it's not sustainable precisely because as soon as people aren't willing to take the extra shifts, the system collapses.
Really, it should be possible to cover all normal shifts (including Sundays, public holidays and unsociable hours) within the normal contracted hours - including leave and other reasonably forseeable absences. Overtime ought to be reserved for unforseen circumstances - but of course that means you have to hire and train more people,) and the existing workforce lose out on overtime pay.
Dragging this back to HSTs - undermanning is one aspect of a lack of system resilience. The tight timetable for getting the HSTs in to release other units is another place where resilience is lacking; if the existing fleets had remained on hire a bit longer, then the cascade could have taken place more gradually and we'd not have as many cases where the Highland Main Line gets a two-car 158 to take 200 people and their luggage. Some services could even have been doubled up, relieving congestion.
But because things had to go off hire so that other operators could use them, that resilience isn't there. We really need to get over this idea that something that isn't being used at full capacity is being wasted.