(I had vaguely remembered more than one such provision, but it was a while ago so I am no doubt wrong on that score.)
Wikipedia would not have been my first choice for back-up, but it was Google’s. You will no doubt now, if you were so inclined, get the actual text and parse it better than I could or Wikipedia does.
I was not trying to inveigh against the evils (or not) of the USA PATRIOT act, merely suggesting that the existence of such a provision could have been the fodder for the fear of jack-booted government thugs evinced by the anecdote in the OP. There are certainly provisions in the act which could be/(have been?) abused, but that is really more of a GD issue.
The OP was discussing “searches” in the context of “breaking into your house” and “pinning the crime on thugs.” A pen-trap register warrant does not authorize law enforcement to enter your premises; the information is gathered at the ISP or at the phone switch.
And, of course, if the police agency in question doesn’t plan to ever use what is found in a court of law, then the need for a warrent drops.
It doesn’t necessarily make one more legal if caught, though.
Many things were done in the effort to find Soviet spies in government positions back in the 40s. But the intent wasn’t so much to take them to court and get a conviction, but to identify and isolate.