But is there really any harm in Daily Notes being active even if you’re not using it? Just don’t use it - same for ZK etc. The tiny amount of extra memory used is a small price to pay vs. having to reconfigure these plugins for every vault.
On your other point about different themes for each vault, yes I can see that being useful. Theme and individual CSS snippet toggles should be a per-vault setting. The CSS snippets repo itself however, should be global.
I admire your ambition to want to roll your own plugin to handle this, but I think something this close to the core should be done natively and with full support of the devs behind it. Anything less will most likely just lead to bad things happening.