Yes, I'd say don't use a note taking app for to-do lists. 
I'm glad that Joplin has a little bit of checklist/todo functionality, but it's just not the main focus of the app.
That said, have you tried @CalebJohn 's rich markdown? It lets you check and uncheck boxes using ctrl-click. It can also put a strikethrough on the checked items.
Even in the MD editor there is a button to add a todo item. and if you press enter it creates a new todo on the next line. So really, it's not so bad considering it's a note taking app.
Welcome to Joplin!