I use Guzzidiag for the older Ducatis with certain ECU's.Not entirely true.
If by 'reprogram' the OP means to flash new map/s and/or edit current maps then most modern ECU's are flashable. The term 're-programme' is used interchangeably with 'flashing.'
There are some ECUs that can't be flashed, because they are old or have been locked by the manufacturer.
However, there are numerous companies making a lot of money by flashing/reprogramming the ECU's of many different motorcycles, or selling the software for owners to use.
For example, there is software called Tuneecu which is around $10US and has many maps for Triumph, KTM, Aprilia and Benelli. There is a free flash software tool called Guzzidiag which can be used to flash Moto Guzzis and Aprilias.
Brad the bike boy, who is a member here, has covered a lot of what can and can't be done with different ECU's in threads here.