Will my customer's frequent flyer number and meal request actually reach the airline when they book on my website?

Yes, in most cases both are sent along with the booking, although whether they are honoured rests with the airline rather than with your website.

A frequent flyer number is normally accepted at the time of booking. Your portal collects the airline and the membership number from the passenger, passes it into the reservation, and the airline matches it against the member account. Two things commonly go wrong here. The name on the ticket has to match the name held on the membership, so a shortened first name or a missing middle name can break the match, and some cheap promotional fares earn nothing at all no matter which number is attached. When the miles do not show up, the passenger can usually claim them from the airline afterwards using the ticket number.

Meal choices, wheelchair assistance and similar needs go across as special requests. They travel with the booking to the airline, but they remain requests. Most airlines confirm a special meal quietly and contact you only when they cannot provide it, and several low cost airlines will not take meal requests through the booking at all, because on those flights food is sold separately as a paid extra. A request added very close to departure can also miss the catering cut off.

Ask your supplier which special request types each of your airlines accepts, and make clear to your customer that a request is passed on rather than guaranteed, so that nobody is caught out at the airport.