CLN/DEPS: Clean up post numpy bump to 1.12
- [x] follow-up to #23062 
- [x] tests added / passed
- [x] passes `git diff upstream/master -u -- "*.py" | flake8 --diff`

I stumbled over a place I had forgotten to change in #23062 - `README.md`. And since I recently found some `grep`-like powers on windows with `findstr`, I took this opportunity to have a look through the code base for other things that got missed in that PR.

Turns out there was quite a bit of crusty old code left from before the *last* bump to `numpy 1.9` (the oldest I found was some commented out code due to segfaults for `numpy < 1.5.1`).

Also, since #23062 bumped matplotlib to `2.0.0`, I looked for old code there as well.

There were a few places where it was not 100% clear what the right way to remove them was - I'm relying on a passing test suite to be a good enough yardstick. In any case, this should have a thorough review to make sure I didn't eff something up.

I'll add a more detailed review right away to explain my reasoning behind each one of the changes.