It seems to be a matter of fierce debate. Unfortunately I could not find any reliable English language resources.
What I found so far:
- The author of a pamphlet that played a big part in inciting the murders was paid by William for several years. It is unclear whether the payments began before or after the pamphlet in question was published.
- William refused to prosecute the murderers and in fact rewarded some of them and furthered their careers.
- William mentioned to Charles II in a secret letter that he was willing to get rid of Johan and his "cabal" of followers.
As you can tell, these instances don't really prove anything.
Part 1 of 4
While you are correct in that there is no 'smoking gun', i.e. no decisive piece of evidence of murder in this case, that is not actually not all that unusual in murder cases. While 'smoking guns' are common in Hollywood movies, real-life murder trials are more about building up big dossiers of evidence, either direct, circumstantial, or a combination of both. While each small piece of evidence does not definitively prove whether or not someone commited a crime, all pieces, when taken together, can often give a solid conviction beyond reasonable doubt.
Incidentallly, I would recommend some of the videos of Devin Stone, professional lawyer and better known under his YouTube alias LegalEagle. He deals with the misconception that you cannot convict someone of a crime based on circumstantial evidence alone in this video (timestamped for your convenience).
So, let's buid a case against Willem III. There has actually been some recent scholarship on this: Dutch historian Ronald Prud'homme van Reine, whose biography on Dutch admiral and national hero Michiel de Ruyter I can heartily recommend, wrote a book in 2013 entitled Murderers of Jan de Witt / The blackest page of the Golden Age (ISBN 9789029587457). The book is the most detailed reconstruction of the murder to date, and it deals extensively with Willem III's role, which was certainly suspicious.
Background
First some background for those who are less familiar with Dutch history. Johan de Witt was the council pensionary (one might say the chairman) of the States of Holland, the most powerful of the seven United Provinces. By extension he also generally set the agenda of the States-General, the 'Parliament' of the Dutch Republic, which consisted of representatives of these provinces. A political animal, capable diplomat and general workaholic, De Witt had through pedigree, political maneouvring and administrative capability become the most powerful person in the Dutch Republic in 1653 at the tender age of 28, and by 1672, he still was. While he was never a Cromwellian dictator, he did hold a degree of power that outweighed his position, essentially becoming a sort of combination of foreign minister, interior minister and general secretary.
The Dutch Republic (or more accurately five of the seven provinces) had, after the death of stadholder Willem II (Willem III's father) been in a period where the function of stadholder, traditionally held by a member of the house of Orange, had been deliberately left vacant. De Witt and his sympathisers were in favour of keeping this status quo indefinitely, and sidelining the quasi-monarchical tendencies of the House of Orange. Being more in favor of leaving the power to the States rather than the stadholder, De Witt's party were sometimes referred to as the 'States Party' or 'Loevesteiners', a nom de guerre adopted after members of this faction had been imprisoned in castle Loevestein by Willem II. However, opponents of De Witt's regime, as well as much of the general public, were in favour of restoring Willem III to the stadholdership, and were called 'Orangists' for this reason.
After the Restoration of the monarchy in England (1660) the Orangists naturally drifted towards that country. The restored monarch, Charles II, was Willem III's direct uncle after all. The Statists on the other hand were comprised disproportionately of wealthy merchants, who disliked the growing maritime power and mercantilist attitude of England, particularly after the first Anglo-Dutch War. This meant the Statists more naturally drifted towards France. De Witt himself always tried to pursue a policy of neutrality with both nations. Merchants above all favour peace; after all, war is bad for trade.
When the French invaded the Netherlands in Rampjaar 1672, thanks to this dynamic the general population blamed Louis XIV's initial success on 'treason' by De Witt's States Party. This led to riots in government capital The Hague, which then led to the murder of Johan and his brother Cornelis in front of the Gevangenpoort. Cornelis had been interned there because of (as we'll see) a very dubious charge of plotting the muder of Willem III.
The traditional account
The classic view of the murder, which was taken as gospel by Orangists up to quite recently, was a rather unbelievable account of one of the perpetrators, Hendrick Verhoeff, a silversmith and member of the local militia (schutterij. According to Verhoeff, the day of the murder (20 August 1672) he was constantly walking around cursing and loudly proclaiming he was planning to murder the De Witt brothers, stating:
De Prins boven, de Witten onder, wie anders meynd, die slaet de donder!
Roughly: "The Prince above, the De Witts under [as in 'six feet under']: whoever disagrees, is struck by thunder! [i.e. crazy]"
The colonel of his regiment, Johan Maess, a local patrician (regent) tries to discourage him, as does the mayor himself, but Verhoeff, shouting and cursing all the way, goes on a tirade against the De Witts and promises them that in half an hour, he will bring them both of the brothers' hearts. This, according to Verhoeff himself, terrifies the patricians, prompting one of his colleagues to remark: "When our dear Lord wishes to punish a country, he robs its rulers of their wisdom." Verhoeff then makes his way through a resisting crowd, grabs some sledgehammers from a nearby blacksmith, and breaks open the door of the Gevangenpoort. He drags the ill Cornelis and his visiting brother Johan from their cell, and throws council pensionary Johan de Witt down the stairs, yelling:
Neemt den schelm dan en bruyt met hem voor den duyvel!
Roughly: "Then take the scoundrel and throw him to the devil!"
One might think that the rest of the story is well-known, considering that, as promised, Verhoeff cuts out the hearts of both brothers and keeps them at his house, showing them to his guests. However, something odd happens: before either Verhoeff or his Orangist buddies can kill Johan and Cornelis, two men unknown to Verhoeff show up. One of them, dressed in velvet, presses a pistol to the back of Johan's head, performing a summary execution, while the other simultaneously stabs him in the chest. Cornelis is similarly executed. Verhoeff's men, frustrated, form a ring around the dead bodies and try to shoot them, but the still relatively primitive muskets do little damage: since they are aimed downwards, the bullets simply roll out of the barrels before any shot can be fired.
Who were these two men? Why didn't colonel Maes order Verhoeff to stand down? And what happened to the cavalry regiment that was detached to the Gevangenpoort earlier that day, and was supposed to protect it during the riots?
Other eye-witness accounts
Prud'homme van Reine's main (but certainly not only) source is a collection of eye-witness reports, gathered together in 1705 but written only weeks after the event. Other than Verhoeff's story above, these include accounts by three of De Witt's clerks; by De Witt's personal servant, who was present with him when he was dragged outside by Verhoeff; and most likely also by two of the militiamen, one of whom entered the Gevangenpoort multiple times that day, but did not like using violence against the brothers. The late publishing date is no surprise: publishing before 1702, Willem III's death, would have been too dangerous.
Another important source is a letter and compiled booklet by lawyer Adriaen Copmoijer. Copmoijer's account was later used as the basis for a play ('Hagueian Fratricide or Crazed Joy' by Oudaen), and has for that reason been discredited by historians pre-WW2, but Prud'homme van Reine argues that the account itself is reliable and should not be discredited solely on this basis. Copmoijer was working in his office on 20 August and in the days before, with full view of the Gevangenpoort.