The protection you mention is there, but is designed to prevent one flow killing Homey. It cannot protect from the cumulative load of multiple bad designed flows.
But you are right, well designed flows you can have lots and lots of. The devil is in the details, and I too have caught myself having flows triggering way way more than I imagined. And more often than not the solution is simple once you realize what is happening.
@Marcel_Ubels is right that for instance triggering on stuff like energy changes may happen really frequently depending on the device. So it all depends how many of those flows you have, how many updates the device sends (e.g. qubino’s seem to send every tiny fluctuation) and what you do in your flow. But that isn’t saying flows like these are outlawed.
I agree it doesn’t seem the case here as there are peaks, and other times things seem ok. So it may me a flow that causes some kind of temporal avalanche of other flows. Or it could be an app. I am wary of the three hubs. If they get polled a lot, each have many devices, and at times get polled all three at the same time, this might well explain this behaviour. When that happens many device states need to be updated.