Oh my goodness -- all you lawyers!
Let me try to cut through some of this nonsense by trying to explain how a court works and how a warrant typically will be issued, and who will know it and when.
The clerk of the court is the official at most courts designated to maintain the docket. The docket is the formal record of all proceedings in a given matter. This is one person who manages all the papers for the entire court -- that is, for all of its judges.
There are others who are sometimes called "clerks" who are not this sort of clerk. First, there are people who work for a particular judge. That is, they work in the judge's chambers. They help that particular judge, not the entire court. They are responsible for what happens in the judge's chambers. Second, there are "clerk magistrates." This is an unfortunate title in Mass, but this person is very different from a "clerk of court." This person is like a judge. Anyway, from here on out, I'll refer to the "clerk" as the clerk of the court.
So, when you file papers in court, you usually file them with the clerk. The clerk accepts them, logs them into the docket, and then transmits them to the judge assigned to the case. Usually, you also send a courtesy copy to the judge, but not always. When a paper is filed in this way, the clerk will know about it. Also, if the court keeps a database, it will usually be updated on that database eventually, although most courts are very slow at doing this. Basically, the clerk gets in a bunch of papers each day. They are stamped to show when received and then they go in a big pile, and someone inputs them into the electronic docket. Federal courts do this daily in real time. Many courts have a person do it manually. It can take days or weeks.
Not all papers filed with a court are filed this way. Sometimes, a paper is filed directly with a judge. For example, you're in court, something comes up, and you hand up a paper to the judge. Some judges will say, "file this with the clerk on the way out." Some judges will accept it. When it happens this second way, the clerk will not know about it. Basically, the judge's staff is responsible for getting that document to the clerk's office, which can take a day or a week. Once the clerk's office gets it, it will be logged, but sometimes there is a delay.
A warrant is like the second type of document. It is not filed. Law enforcement or the prosecutor puts together an affidavit (or other evidence) and then brings the warrant directly to a judge or other court officer permitted to sign a warrant. The judge then reviews it and signs or doesn't sign it. Sometimes this happens at the courthouse. Sometimes this happens in the foyer of the duty magistrate's house in the middle of the night while a detective stands on the porch.
As a result, the clerk of the court will have no idea that a warrant has issued unless and until it is brought to him. In some places, this falls through the cracks and takes a while. Sometimes it's the prosecutor's responsibility to get it the clerk. Sometimes it's the judge's responsibility. Similarly, the clerk of the court will have no way to know about unsigned warrants. They don't get filed (at least not usually -- they may later become relevant to some issue and get filed as attachments to other documents).
In addition, every jurisdiction has rules that permit warrants to be issued without them becoming public -- specifically so the defendant isn't alerted until they are served or executed, or for similar reasons. These rules are different everywhere. In some jurisdictions, they sit in the judge's office for a while. In others, they are formally "sealed" -- which means they are filed but filed in a secret way. Other jurisdictions allow warrants to be held by the prosecutor and put in his back pocket, without filing them with the clerk. This is not common, because often the prosecutor will need to claim some kind of exigency to get the warrant which is inconsistent with back-pocketing it.
So, what does it all mean? It means that the clerk will almost never know whether a warrant has been prepared and presented. The clerk may not know that a warrant has been signed for a few days. After a few days, they should know. Finally, there are many different authorities who have power to issue certain types of authority, and many different courts may have overlapping jurisdiction. Police and prosecutors are not always careful about from which judicial officer they obtain a warrant -- what the police care about is that evidence or persons seized will not later be suppressed or vacated. So long as they act in good faith on a warrant, that won't happen, even if the wrong authority, court, or jurisdiction issued it.
At this point, I think it's pretty clear that the Attelboro district court did not issue a public warrant. By now, the clerk would know, and it sounds like he is on record as saying he is not aware of a warrant. Could it be sitting in the box of the magistrate who issued it, not yet transmitted to the clerk's office? Theoretically. Unlikely. Could one have been prepared and submitted and either not signed or signed and then withdrawn with the clerk knowing it? Yes. Could another jurisdiction have issued a warrant (or sealed a warrant) and the clerk in Attelboro not have know it? Sure. I doubt it, but you never know.
So, and this is crucial, I am not making any conclusions here about what this does or doesn't mean regarding Aaron Hernandez. It just seemed to me that some of you were making some assumptions about matters the required a fuller explanation.