Like many bots, Daedalus' features are mostly divided into modules, with the exception of some things like logging. Each module contains functionalities that are of a similar purpose or integrate with each other. For example, all manual moderation commands (ban, kick, slowmode, purge) are grouped in the Moderation module.
Disabling a module disables all commands within it as well as most automatic or user-triggered features within it (for example, disabling automod disables message scanning entirely).
You can disable the core module and settings commands if you want, though it will prevent you from modifying some settings that will still be used by the bot (that is, disabling settings commands does not make the bot act as though those settings are not set).
Log events/changes in your server.