That is actually how it works. The FBI it not, by and large, dumb about investigations. They are arguably one of the best in the business. Part of that is they know that you can't always get the evidence you want. So they'll subpoena records, but so long as you make a good faith effort to comply, they tend to be happy.
At work (a university) we get FBI subpoenas once and awhile. Quite often it is for shit that we don't have, like someone's e-mail from a long time ago. We look, see if we have a backup, and if not let them know. They are then on their way.
When people get in trouble is when they try to jam them up or break their own rules. Like if you have a company rule that says you keep all documents of X type for Y years, and they are asking for something that is Y-3 years old, they may well get miffed and go after you if you don't have it. However if you do not retain document type X, and there is no law requiring it, simply letting them know that will make them happy.
This isn't to say nobody ever gets a bad/vindictive/whatever agent that tries to create problems, but if you were to do a study, I bet you'd find that most of the interactions are very professional and they are perfectly understanding if you don't have the information they want. In the cases where a hissing match started it was because someone had the information and refused (or made it sound like that) or otherwise jammed them up.