How do I make Guake use my Zsh command history?

Guake is a terminal emulator. As such, it doesn't store the command history anywhere (it doesn't even have a clue what a command history is). It launches your shell, and the shell does the rest.

It could be that, for whatever reason, Guake launches a different shell, e.g. bash instead of your preferred zsh. It could also be that it launches zsh with some different settings, e.g. different argv[0] which causes zsh to behave differently (e.g. bash behaves differently if you start it as sh; not sure if zsh has something like this too).

Another explanation could be that when Guake hides its window it doesn't terminate the shell running inside, the same zsh keeps running there and is shown you again when you invoke Guake again. That is, zsh did not write its history in between and did not read what other zsh instances wrote there (exactly as if it was a "regular" terminal emulator whose window you minimized but didn't close).

In your terminal, type 'guake'. When Guake launches, right click and click on preferences then click locate shell tab. On the shell tab, select /usr/bin/zsh. This will set your default shell to zsh, subsequently storing your code to zshrc_history. I hope this helps!