Can I spawn an AGPL executable (mupdf for example) from my python based Apache-2.0 project?
Note: I'm not linking to it, merely calling the executable from the shell.
Yes, what you are doing is ok.
First of all, by spawning the AGPL executable as a separate process, the two programs are considered independent works as far as copyright is concerned and their licenses do not affect each other.
But even if your project would be considered a derived work there is no problem. The Apache license is compatible with the AGPL, so you can have an application that contains code under both licenses. In this case, you may have to take some action to meet the requirements of both licenses, like offering your users the option to download the complete software according to the AGPL license.