So in the old days when WordPress updated you got the whole shebang and deleting Akismet after every time was deadly boring.
Things had slightly improved since then (partially driven by minimizing traffic it takes to serve update to everyone), but process also got more complicated.
Now there are multiple versions of update archive that core might receive and apply. They are (at least):
- partial (only differences, I think this ignores content folder)
- new bundled (only includes new things in content folder, such as annual theme)
- no content
Now on most updates you are likely getting partial or new bundled. It means effectively that once you remove bundled plugin/theme it won't reappear. However new one will, for example WordPress 4.1 added Twenty Fifteen to my install, but not older themes I had previously removed.
So the old things stay removed already. To also disable new things there is a
CORE_UPGRADE_SKIP_NEW_BUNDLED constant, which is what you might be thinking about.