Yes. Squarespace generates a certificate for each custom domain and subdomain connected to your website. This also true for the www version of your domain, if you're using it separately from your naked domain.
If you're using your subdomain as your site's primary domain, uncheck Use WWW Prefix to prevent certificate errors.
If you have a third-party domain, ensure that it’s connected in your site’s Domains panel and not forwarded or pointed to another location.