There will be no fine to pay as this case was not brought to court after an investigation by the Dutch tax authorities, but by an assessment of the tax return the pilot in question had filed himself. It is a dispute over his status as self-employed / employee rather than a criminal case over tax-evasion. He will simply have to pay tax as an employee in stead of a self-employed individual.
The more interesting consequence is what the Dutch government will do next. If Ryanair is deemed to be the employer of pilots based in The Netherlands, then Ryanair is liable for the employer part of social security premiums and labour taxes applicable in The Netherlands. Not a huge number of pilots indeed, but if Ryanair has to pay these employer premiums and taxes for all their crew based at EIN it amounts to a nice sum of money and automatically puts all this crew in the Dutch social security system as employees (and entitled to all applicable benefits, such as sick pay etc.).
That is a precedent if it happens, and in previous cases like Marseille Ryanair pulled their crew out of France quicker than you can say: 'bogus self-employment'
I find it incredulous that either a large corporation (RYR) or a supposedly intelligent individual could genuinely believe that stating 'self-employed' was legitimate. My wife is registered as a ZZP (self-employed) in the Dutch system, as a freelance dance instructor, and it is abundantly clear when filling in the tax returns (and looking at the guidelines for eligibility) that working full time for a single 'client' does not qualify!