I am creating a template site on my server that I can quickly duplicate to build new clients sites. I was going to create multiple templates, but then I thought if I am just changing a couple sections on the site why not hide the element (or variation) of that section that I am not using. My question is will this slow down or affect the site negatively in any way by having elements on my site that are set to display none?
I would use conditions to show the sections or not.
Display none I would not use because the data is still loaded and it is quite easy to unhide these sections in the front end by the users if they know how.
You could for example make an options page with ACF and define there which sections shall be shown or not shown.