Can my customers buy extra baggage for their flight after they have already booked?

Yes, with some airlines, but not with all of them. Adding a bag after the booking is already made depends far more on the airline holding the ticket than on your portal. Low cost airlines usually make this easy, because extra bags are a large part of how they earn, and many of them allow a bag to be added right up to the day of travel. Full service airlines are more mixed, and some of them only allow it on their own website or at the airport counter.

Where it is supported, your staff open the booking on the portal, add the bag, take the payment from the customer, and the airline updates the ticket. Where it is not supported, the booking itself is not affected and the customer can still add the bag directly with the airline, usually during check in, although the price at the airport is normally higher than the price paid online in advance.

It also depends on the supplier behind that fare and on your plan, because not every supplier passes these later sales through, even when the airline itself allows them. If your portal does not show an option to add a bag on a particular booking, that usually means the supplier for that fare does not support it rather than the airline refusing the request.

Open one of your recent bookings on the portal and see whether an option to add baggage appears, and agree with your staff how they should handle these requests so that nobody promises a customer something the airline will not honour.