Count distinct instances of a SKU and count all items in all instances containing that SKU
You can use a window function with the COUNT() function in a CTE or subquery to get the total Line_Item_ID count per Sales_Order_Id or even just group it separately at that point, and re-join it to your existing query with a SUM() on top of it to get the total Line_Item_ID for each SKU like so:
WITH CTE_LineItemsPerSalesOrder AS
(
    SELECT sales_order_id, COUNT(1) AS LineItemsPerSalesOrderCount
    FROM Table
    GROUP BY sales_order_id
)

SELECT T.SKU, COUNT(DISTINCT(T.sales_order_id) as Order_Count, 
    SUM(C.LineItemsPerSalesOrderCount) AS Line_Item_Count
FROM Table T
INNER JOIN CTE_LineItemsPerSalesOrder AS C
    ON T.sales_order_id = C.sales_order_id
GROUP BY T.SKU
ORDER BY T.SKU

Feel free to rename and reformat the casing of the syntax I used, as needed.