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I use WordFence which is pretty good for the free version. Also really hammer down the folder permissions. I run a server with mod-ruid2 which runs apache/PHP with the users ID instead of the webserver ID. Means the wp-content folder can be run with 755 instead of 775 or 777.
Also as has been mentioned rename the /wp-content folder to something like /assets - there's additional steps & wp-config.php settings needed. Links on the interwebs.
And also move the wp-login page, again interwebs for the code for the functions.php file.
I use my own bespoke skeleton theme https://github.com/ontiuk/iPressRD2 which also pretty much strips all the garbage that WP injects into the header - and telegraphs that it's a WP site - including bloody emojis.
The functions.php file is in the theme, so not applicable to core WP updates. I generally use it to create a standalone theme for personal/client projects - no page-builder garbage.
For commercial themes e.g bloated multi-option page-builder themeforest offerings, and those in the WordPress repository that have the update theme option in WP admin, then yes, I recommend using the theme as a parent theme always and creating a child theme for development. For bespoke standalone themes, then it's not really required, though I do do it for client projects.
2000 ! Holy wordpress.That's a lot of sites. I've already installed it on my sites. Seems fab. Securi seems to be the other one that comes up a lot as an option.