Further to this, although I am only speculating, was both the Aircraft and Pilot in Command capable of legally entering Class A?
Even if the pilots and planes were IFR capable, you don't get to enter the Schiphol TMA over there without a very, very good cause.
And under the act you can be prosecuted for "disturbing" wildlife. So if one bird takes flight while you are flying over and one of the park rangers suspects a causal relationship between the two, you're screwed.
If they can read your callsign, that is, because this particular area currently happens to be in/under the Schiphol SRZ so your mode-S transponder, while mandatory, has to be switched off.
Is there a statutory prohibition on overflying this reserve?
No, but there is a statutory prohibition on disturbing the wildlife in this reserve. And that statue has no vertical limits. Theoretically you could be prosecuted while overflying this reserve at FL300, as long as a park ranger finds that you disturbed an animal. And that's why this case is so important: We're trying to establish what the vertical limits of this wildlife act are.
And remember that this is not just some local Dutch case. This legislation was all forced upon us by EU legislation so at some point in time the same crazy lawsuits may happen in other EU countries. What gets decided here may well be influential in how similar laws in other countries may be interpreted.
If not then their hands are tied and a case is to heard against the relevant authority for placing the lower limit of Class A in such a way it conflicts with pre-existing limits.
Although the judge noted that the laws clearly conflict, and called upon the Dutch government to resolve this situation, I suspect that this rather low-level judge was simply not legally able to weigh one law against another. The public prosecutor was basically able to prove that the wildlife was disturbed in the legal sense of the wildlife act, so the judge at this level had no other way than to find the defendants guilty. That they were conforming to all aviation laws and customs at the time was not deemed a valid defence.
(I guess it's kinda similar to performing a drive-by shooting and then using the fact that you adhered to the speed limit at the time, so were complying with road transportation laws, to claim you cannot be prosecuted for murder.)
Weighing laws against each other and thereby establishing limits on the reach of various laws is handled higher up. So hopefully this is just the opening move.