WP Multisite and plugin network enabled

I try to initiate network-enabled plugins but some sites do not need this option like menu, https://woocommerce.com/. As plugins add additional code and code insertion, can be managed code inside functions.php or JS file to block some added code?

I recommend that you get in touch with people from the woocommerce forum at https://wordpress.org/support/plugin/woocommerce/