Do orphaned HKCR root keys cause significant slowdown of os performance or is the effect limited ?

What do you mean by an orphaned HKCU key?
Could you provide an example?

There are a whole load of things in HKCU and some of them will slow down Explorer if they are correctly installed.

I think it is about HKCR and not HKCU.
Yes when the packages pile up then the registry keys are orphened.. When the registries grow, then the performace will be degraded...