Because when the time comes, it will invalidate the MOT. Without the software alterations the emission ratings remain bogus and a certificate will be needed to prove the upgrade has taken place.
Maybe worth mentioning that the gas mentioned (Nitrous oxide) is not even checked on the MOT!!
I don't expect the values of these cars to be affected in the longer term, Yes they are slightly down at the moment but things will even out in about a month or so. Toyota's had problems with their brakes years ago and residual values remained constant.
If it's NO emmisions that's affected and not CO2 then motorists wouldn't be able to claim they were misled as the CO2 emmisions as given by the manufacturer wouldn't alter.