because officially they aren't employees of Ryanair
Bet the taxman would have something to say about that!! Well, they would under UK tax and employment law but if Ryanair pilots are employed under a different country's regime, then who can say. If they're "employed" under a contractor scheme (i.e. limited company under IR35), then professional advice should definitely be obtained!!
If Ryanair are operating under another country's rules (i.e. Ireland's), any self-employed pilot would not be making a UK VAT-able supply to Ryanair and so the rules could be entirely different.
Cheers
Whirls