They are as common as non religious schools in the Netherlands. And, they have to meet the same standards.
I see no harm in them. And, they are most of the time not of a fundamentalist orientation. In my village there is a catholic primary school, a non denominational one, and one that covers most of the christian orientations. On all schools, there are kids of every possible denomination.
The non denominational is not doing that well in educating at the moment, and, thank goodness, parents can choose between two other primary schools.
If anything, it has made my kids think more critical, to be at a christian school. And, I don't mind.
For some kids, the school they are on is the first place where they see there are other interpretations possible than the ones they learn at home (We've got a few families that belong to a kind of cult) They would never see this other interpretation on a non-denominational school. In fact, that is why lots of kids from obscure sect like christian denominations visit a non-denominational school. That would not pervert their beliefs, because it would not mention it.
First thing I asked at the school was how zealous they were. Had it been one of the few zealous schools, my girls would probably have gone to the catholic school, because the non-denominational here just sucked.