So, if you want to minimize the re-renders of the items, you need to make sure of a few things

Memoize the component

You can use React.memo on the component you want, which will prevent re-renders when the props/state do not change.

so, use

export default React.memo(Item);

instead of

export default Item;

Make sure the props are the same

When you render the Item component you pass deleteItem as a prop with a value that is received from the App component. However, this function is not a stable (it is redefined each time the App component renders. And since the App holds the items state, it will rerender after each deletion. This will trigger a new deleteItem to be defined, and that will cause the Item to re-render.

To make this stable, you need two things.

1. to use React.useCallback which re-uses the same function when its dependencies remain the same.
2. use the function form of the setItems

so, instead of

const deleteItem = (newItem) => {
  const newItemList = items.filter(
    (item) => item.reference !== newItem.reference
  );
  setItems(newItemList);
};

use

const deleteItem = React.useCallback((itemToDelete) => {
  setItems((currentItems) =>
    currentItems.filter((item) => item.reference !== itemToDelete.reference)
  );
}, []);

You also have an issue in your code, where you .map the data but then before returning each Item you push it in an array and return that instead. Just return the <Item ..>

So instead of

    {props.data.map((item, index) => {
      const newList = [];
      newList.push(
        <Item
          deleteItem={props.deleteItem}
          key={item.reference}
          item={item}
        ></Item>
      );
      return newList;
    })}

do

    {props.data.map((item, index) => {
      return (
        <Item
          deleteItem={props.deleteItem}
          key={item.reference}
          item={item}
        ></Item>
      );
    })}

Updated codesandbox with all changes: https://codesandbox.io/s/twilight-water-9iyobx

It sounds like you want to iterate over your array of objects to produce rows of data in a table with the last cell in each row to be a "remove" button that removes the row. And you can do that. No need for useEffect.

const { useState } = React;

// Pass in the data
function Example({ data }) {

  // Set the state with the data
  const [ tableData, setTableData ] = useState(data);

  // When a remove button is clicked `filter`
  // out those rows that don't match the row id
  // and reset the state
  function handleRemove(e) {
    const { id } = e.target.closest('tr').dataset;
    const filtered = tableData.filter(obj => {
      return obj.name !== id;
    });
    setTableData(filtered);
  }

  // Create some rows by mapping over the
  // table data
  return (
    <table>
      {tableData.map(row => {
        return (
          <Row
            key={row.name}
            row={row}
            handleRemove={handleRemove}
          />
        );
      })}
    </table>
  );

}

// Create a table row and populate the cells
// with the information from the row object
function Row({ row, handleRemove }) {
  return (
    <tr data-id={row.name}>
      <td>{row.name}</td>
      <td>{row.reference}</td>
      <td>{row.description}</td>
      <td>
        <button
          onClick={handleRemove}
        >Remove
        </button>
      </td>
    </tr>
  );
}

const data = [
 {name: "NAME 1", reference: "REF 1", description: "LOREM IPSUM"},
 {name: "NAME 2", reference: "REF 2", description: "LOREM IPSUM"},
 {name: "NAME 3", reference: "REF 3", description: "LOREM IPSUM"},
 {name: "NAME 4", reference: "REF 4", description: "LOREM IPSUM"},
 {name: "NAME 5", reference: "REF 5", description: "LOREM IPSUM"}
];

ReactDOM.render(
  <Example data={data} />,
  document.getElementById('react')
);

table { border-collapse: collapse; border: 1px solid #565656; }
td { border: 1px solid #dfdfdf; padding: 0.5em;}

<script src="https://cdnjs.cloudflare.com/ajax/libs/react/17.0.2/umd/react.production.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/react-dom/17.0.2/umd/react-dom.production.min.js"></script>
<div id="react"></div>

When updating the state you need to spread the previous state first before you update it Example:

const deleteItem = (newItem) => {
  const newItemList = items.filter(item => item.reference !== newItem.reference);
  setItems(prev => (...prev, newItemList));
}