I'm sorry for the confusion here - if the documentation you're reading is referring to master canvases, you're reading documentation for version 4; the corresponding feature in version 5 is "Shared Layers".
You can download the documentation for version 5 from this link:
http://www.omnigroup.com/applications/omnigraffle/
I'm not on the OmniGraffle team, so I can't speak to why any keyboard shortcuts got changed, but I can say that we only change them when we absolutely have to, because we know exactly how annoying it can be to re-learn muscle memory.
I know a couple of years back, Apple released an updated version of their Human Interface Guidelines which specified several new keyboard shortcuts that were now reserved by the OS and shouldn't be used in third party applications. Because we like to be good citizens on the OS, we changed our own shortcuts; sometimes we had to find shortcuts with combos like the ones you're upset about.
Again, I don't have any specifics, so I can't say for sure that this is what happened; I can say that calling for the folks who
do know to be fired probably isn't going to motivate them to post in this thread.