Diagnosing what hardware exactly is then a matter of stopping and starting whatever processes eg, if you are doing something with a video camera and writing the data to disk, try doing the same thing but throwing the data away instead (eg, to /dev/null). This could be the hardware itself malfunctioning or the driver which controls it.

A high load average is more than 1.0 if you notice that consistently while the CPU usage is less than 100%, it indicates a lot of waiting on hardware is going on.

Top and htop both report load average and overall cpu usage at the top. You can more generally infer significant IO/hardware related issues if the load average is high while the CPU is relatively idle.

I suspect you have it backward when you say, 'clearly the system isn't coping' in fact the system is mostly idle because there is an I/O bottleneck. Specific I/O bottlenecks are found by inference this way (timing the round trip). This is time that involves neither kernel nor user space activities so it is not reportable as an activity (because it isn't an activity of the processor), although it can be measured on a clock (the same way a network request-response cycle can be timed on a clock, although it mostly does not involve any kind of activity by the local computer). However, waiting on disk access is not necessarily time spent using the processor. WRT your example of waiting for disk access, in so far as this time is active processor time, it is reported as part of the time used by the process doing the deed. Kernel threads do not at all represent the totality of what the kernel is doing, most of which is in service to specific userland processes. htop doesn't, but that can be toggled with shift-k (see the htop man page WRT kernel threads). Kernel threads usually have names like kworker and kthreadd and have other special characteristics by which they can be identified (read the link) but they are unlikely to have anything to do with what you are doing. kernel daemons (although there are fundamental similarities, in context do not confuse this with process 'threads' generally, which exist in userspace). There is such a thing as kernel threads aka. I'm not sure what 'kernel processes' you are talking about.

Top htop