So, there are Imperial Warrants, issued by Archdukes enforced/enforceable at the Domain level and so on down from there. How low in the "highest levels of government" does the power to issue Imperial Warrants extend?
And then there are IMPERIAL Warrants issued by the Emperor enforced/enforceable across the Imperium.
There are probably very very few IMPERIAL Warrants issued. And these would (should) only be available directly from The Emperor and probably only issued to the highest nobles and officers and at Capital. Archdukes, Dukes, and perhaps IN Grand Admirals. Their scope is such they would not be issued/used for "minor" matters. If I had to give a hard number I'd say an average of 1 per year. There would be more during Imperium wide crisis, and fewer in times of peace and stability. Decades may pass without a single one being issued. Some Emperors may reign without ever issuing one.
There would be a few more Imperial Warrants issued by Archdukes. Again probably only available in person at the Archduke's base of operations. Issued to Dukes, Counts and perhaps IN Admirals. The more limited scope (Domain level) and immediacy would see more issued. Something on the order of 2 to 12 (yes I think in D6 for CT

) a year maybe. And while not issued for "minor" matters some of the concerns would be minor on an Imperium wide scale.
Then there would be the hundreds or more Imperial Warrants issued...
...by Dukes (for Sectors?) to Counts, Marquis, and perhaps IN Captains.
...by Counts (for Subsectors?) to Marquis, Barons, and perhaps IN Commanders.
...by Marquis (for Worlds?) to Barons and Knights (maybe).
I don't think Barons would have the power to issue Imperial Warrants.
So a nothing nobody (like a PC not a high noble or IN Officer) showing up with an Imperial Warrant is not going to be taken at face value and had better have a very good story to go along with that Imperial Warrant if anyone is going to believe them. A Baron might pull off flashing a Ducal Imperial Warrant, and an IN Commander (retired even) wouldn't be deeply questioned employing County Imperial Warrant.
Just have an ex-Merchant Free Trader crew try getting some lifesupport and fuel at a starport on an IMPERIAL Warrant though and see how quickly the local forces "invite" them to explain the situation and provide some proof or face the full force of Imperial Justice.
That'd be my quick take on it.