There are two use cases of shadow DOM as far as I can see:
You control the the shadow DOM solely through your hosting custom element (like in the answer of @Penny Liu). If you want make sure no other script should call and alter the nodes than this is your choice. Pretty sure some banking websites use this method. You give up on flexibility though.
You just want to scope some parts of your code for styling reasons but you like to control it via document.getElementById than you can use <slot>
. After all, many libraries rely on the document object and will not work in shadow DOM.
Back to the problem, what you probably did was something like this:
shadowRoot.innerHTML = `...<script>document.getElementById('target')</script>`
// or shadowRoot.appendChild
This is NOT working! And this is not how shadow DOM was anticipated to work either.
Recalling method 2, you SHOULD fill your shadow DOM solely by <slot>
tags. Most minimal example:
<!-- Custom Element -->
<scoped-playground>
<style>some scoped styling</style>
<div id="target"></div>
<script>const ☝☝☝☝ = document.getElementById('target')</script>
</scoped-playground>
<!-- Scoped playground has a shadowRoot with a default <slot> -->
...
this.shadowRoot.innerHTML = "<slot>Everything is rendered here</slot>";
...
More advanced <slot>
examples can be found at:
https://developers.google.com/web/fundamentals/web-components/shadowdom#composition_slot