I think it is important to leave the header and footer in. IMHO.
But. I sometimes subdue it when I am presenting a document to other people. So, I encourage you to leave it as is except for certain circumstances where you want them to appear more as a watermark. This is how I do it. Add this between <style> tags in your markdown document, or stick in in a .css file and import it when you need it...
/* Subdue the top-header branding */
body.page-note nav.navbar { opacity: 15%; }
/* Subdue the JoplinCloud footer */
body.page-note > div.footer { opacity: 50%; }
Now, I am using the paid-for JoplinCloud service. If you are self-hosting and all that, I feel less evangelical, and you could do a display: none; in there instead of the opacity settings. Do what you feel makes you the most comfortable.