What are the ways in which installed software can negatively impact OSX speed over time?
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.