That's how the microbitcoin.net app I developped is working to generate a new address for each new invoice.
You need a watch only electrum wallet to get payment notifications but akaik an electrum API is still to be developped.
Anyhow, for a webshop, checking the electrum wallet from time to time is sufficient at this point.
If your project entails withrawals in bitcoins, you may want to consider imposing a lead time and checking the withdraws manually or via an audit node.
Maintaining a hot wallet for instant withdraws is a risky business unless you are ready to spend on infrastructure.