How do I prevent macOS from thinking a folder is a file?
It’s thinking it has an extension because you’re giving it an extension.  

Anytime you end something with a .whatever you're giving it an extension.  This is a convention across all operating systems and not limited to macOS.

Instead of using dots as a separator for dates, use a dash or an underscore. You don’t  need to do this for all folders all at once, but with a little bash scripting magic and using a utility like sed or awk the renaming of the files/folders can be done automagically.