With info provided, I can see a few things it might be:
Rewrites
Review your .htaccess rules, the rewrites (arguably) don’t do a lot of work on the home page – which may be why your issue is inner-page only.
Run a flush or visit your wp-admin > Settings > Permalinks and [Save]. The rewrites which WooComm may be using may be doing something unexpected.
Database
It could be missed http database values (with WooComm) you can do a find and replace on the database. With wpcli
you can see what’s non-https with
wp search-replace 'http://example.com' 'https://example.com' --dry-ru
Theme
If you do believe it to be your theme, though unlikely unless custom theme, you can browse the source code of your theme and look for hard coded values, with command line:
grep -r 'http://' /path/to/wordpress/wp-content/themes/
Debug
Be sure to turn on WP_DEBUG
and check your servers error logs incase the 404s are just hiding a simple php or setup error.
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