Question:
As for my experience, you must go for subdirectory installation of each wordpress/woocommerce instead of using WP multisite, theres so much trouble in there.

Answer:
Trouble probably because you are not to familiar with WP Multisite 🙂
WP Multisite are great and the simplest solution to mass produce similar shops in sub domains, domains or folders, you can just copy entire sites to a new domain. You will not get a common shopping cart or checkout for all the shops, but with a plugin like this: https://woomultistore.com/ , you can at least have a global order view and common product stock. And it will also offer common cart for many stores in the future.