Commands in the command palette are hidden from you if the command that implements them is disabled or doesn't exist; you can only see commands that you can actually execute right now based on the current context.
As far as I can see, the reason for your problem is that
git_gitk_all are no longer commands that appear anywhere within the package; the only one that remains is
If I had to guess, I would say that those commands were removed from the code base but not from the commands file. It might be worth logging an issue or at least pinging the author to see what the official stance is supposed to be.