The problem with having an ND on all the time is when you point the camera in a direction which causes your shutter speed to drop and your ISO to rise.
I know: what I was saying is that even is this higher ISO situation, you are no worse off than with those older, lower ISO sensors, due to the improved usability of the newer sensors at higher ISO speeds being enough to off-set the light loss due to an ND filter. For example, the changes that move minimum ISO speed from 50 to 100 (improved QE through BSI, better micro lenses, etc.) also mean that ISO 800 is as good on the new sensor as ISO 400 was on the old, and so on up. (Probably a bit better in fact, due to other improvements that do not raise the minimum ISO speed.) So even if you use a 1 stop ND filter to emulate ISO 50 when set at ISO 100, so that you need to use ISO 800 where the older sensor would have needed only ISO 400, you are no worse off than with that older sensor. It is just that to both
(a) get the low light performance advantage that the newer, more sensitive, sensors have over the older ones and also
(b) be able to handle "very low exposure index" situations
requires the extra fiddle of putting an ND filter on and off.
Of course it would be very strange to use a camera with always-on ND filter, but even that weird usage would be better, not worse, than using one of those older, less sensitive sensors, at least with an EVF that can adjust the viewfinder image brightness for the presence of an ND filter.
P. S. Another little bit of good news: with some recent cameras, like Olympus CSCs, the base ISO speed (minimum safely usable exposure index) is significantly lower than the minimum setting on the ISO dial: they are calibrated to give more raw highlight headroom than the minimum
suggested by the ISO 12232 standard. So a camera like the EM5 with a minimum ISO dial setting of 200 has a minimum safe exposure index of about 120-130.