What are the ways in which installed software can negatively impact OSX speed over time? Applications installed on macOS are not always completely self-contained. Sometimes they write files in multiple locations outside their .app bundle, taking up space that they sometimes occupy even after we uninstall them. 

What I'm more interested in with this question, is understanding the ways in which an application (even when not launched), can slow down the OS (eg. boot time, shutdown time, GUI responsiveness, app launch time).

I know that applications (both malicious and not) install:


kexts
Login Items
LaunchDaemons
LaunchAgents


Beyond these four, what are other ways in which installed software can negatively impact the performance/stability of the overall OS?
One notable absentee from your list is the category 'plugins'. I.e. additional software that runs within existing software on your Mac. It could be browser plugins, plugins for Microsoft Office, or many other types of plugins.

Besides that there's not really supposed to be other ways if you're only installing "well-behaving" software.

If you install software that is more or less malware, it could wreak havoc with your system by modifying system binaries, system configuration, system firmware or by creating other ways like LaunchDaemons/LaunchAgents to ensure that its own software is run on boot and continues to run.