SQL CE is very convenient for deployment and is ok for small to medium traffic sites but is not anywhere near as robust as SQL Server. For a serious business class web site I would use MS SQL. You will get much much better performance and stability with SQL Server.
If you need WebStore that is another reason to go with SQL Server, because we don't have a data layer for WebStore implemented for SQL CE and there are no plans to implement that any time soon. WebStore is a relatively immature feature, when it becomes more mature we may implement some additional data layers but that is probably a long way in the future. If we implement more data layers now it becomes more work to evolve the feature and make changes and would only slow down progress. Besides that ecommerce is business and I would not run my business on SQL CE, so that would be a low priority for WebStore.
Best,
Joe