Great question! The short answer is no, but let me try to explain
For a correct interpretation it is important to understand the Dutch educational system. The school compares the students' grades to those of other VWO-students; which is very different from comparing the grades to the national average (which is impossible in the Netherlands).
In Secondary Education (which starts after 2 years of 'kindergarden', 6 years of primary (formally kindergarden is part of primary); so at around age 12) students are divided between different streams/tracks according to their abilities:
- A small percentage goes to 'practice-oriented education' (the lowest level; these students are not expected to complete formal education);
- over half of the students goes to VMBO (preparatory vocational education) - a 4 year program; students are expected to continue their education in a vocational program (community college-type) which might take 2-4 years to complete depending on the level;
- about 25% goes to HAVO (higher general secondary education) - a 5 year program; students are expected to continue their education in a higher professional education institute (hogeschool; (fach)hochshule; university of applied sciences; comparable to a post-1992 university in the UK);
- and a little over 15% (this number is increasing, probably around 17-18% these days?) goes to VWO (preparatory university education) - a 6 year program; students are expected to continue their education at one of the (research) universities.
[As a side note: it is possible to move up (or down) from one track to the other both in secondary education as well as in tertiary education]
Within this highest level (VWO) a distinction is made between atheneum and gymnasium. The only difference is whether the classical languages (latin & greek language and culture) are taught (in addition to the standard VWO program). Between 1/4th and 1/3th of the VWO students do gymnasium (so at max 6% of the population).
Amalia and Alexia are attending a 'categorical gymnasium' which means that all students at their school attend gymnasium. It is also possible to do gymnasium at a secondary school that offers HAVO, Atheneum and Gymnasium tracks. The reason why the average grades (at the final exam) for latin and greek are typically lower for students at the categorial gymnasium than for those at other schools that offer gymnasium, is that the students who have low grades in latin and greek at a 'broad' school can easily switch to Atheneum within the same school, while those at the 'categorical' school would need to switch schools, which means that they typically stick with either Greek or Latin just to be able to stay at the school even though they struggle in these subjects.
So, the grades that the school shows should be interpreted in the light that it compares the results of the best 15-18% of the students (and for latin and greek the best 6% at max; taking the above into account). Furthermore, it is important to understand that people in the Netherlands are not very much focused on grades. Most important is the level (track/stream) that you attend and graduating within the allotted years. The school for example prides it self in an extremely low number of students that have to repeat a grade (which typically has the side effect of lowering the average grade at the final exam).
Finally, the princesses went to a public school for their primary education, so I am pretty sure that the denomination (being protestant-Christian) was not a deciding factor. According to the king and queen Amalia picked the school herself (her cousins who also attend secondary schools at VWO level in The Hague made different choices; Alexia apparently wanted to join her sister). She visited a few different schools in The Hague that offered the gymnasium track and landed on this specific one. Currently, she is even in the gymnasium-plus group; a selection of students that do very well at school and are offered additional classes (so far it is Chinese; but in later years she will most likely also take classes at Leiden University as part of a PRE-program that is offered by the University to excellent students in their final years of VWO) to keep them challenged.
Yes, I recognised the photo from the family portraits too. I think this is one of my favourites of Amalia though - it's really captured her features well. 
