There could be several reasons for not arresting these "spies". First, there might have been just suspicions but no real evidence, something that would make prosecuting these men problematic and also cause a significant diplomatic struggle for the Dutch. Secondly, the evidence itself might expose sources and methods that the Dutch would not like to be exposed in a publicly prosecuted legal case. Third, the NRC article suggests that these individuals might have been two earlier evicted Russian embassy employees, in which case they might even have been immune to arrest.
The timing of these allegations are at best suspect. If the allegations are true, it would definitely not look great on Russia. But it might have been about Russia trying to get insight into what they are up against in the whole Novichok debacle. Not nice, but something (m)any governments might try, in a case like this.
It should also be noted that Holland is not an impartial party when it comes to Russia. One of Holland's largest companies, Royal Dutch Shell, bought exclusive concession rights (for several decades to come) to natural resources in the Ukraine, most of which became inaccessible to them after the regime change in Kiev and the subsequent separation of Crimea and the eastern part of the country that it triggered. Shell, just as key American players who made similar deals, will not be happy about how events unfolded in the Ukraine. Furthermore, Shell has a substantial leverage within Dutch politics and government. Of course, none of that proves that the Dutch can not be trusted, but it might be wise to at least not blindly believe whatever Russia related news comes from them.