These cases arise because of legislation that has not been updated to account for new technology. If you're charged with regulating a newly-liberated telecom market in 1992, it makes sense to require "telecommunication providers" to register as a first step to monitor developments in the market.
With the internet, you suddenly have thousands of people and companies that fit the letter of the law. You tell the politicians that maybe something should be done, but it doesn't really appear to be important so they'll wait to stick it into a general overhaul of the legislation that's on the horizon, and do more urgent stuff in the meantime.
But, as the guy/gal tasked with this register, all that matters is the actual law, and you're pretty sure it applies. What now?
You could just disregard the law. You probably won't even get in trouble, because it's unlikely they'd notice anyway, nor would it cause any harm.
But sending out these letters defying common sense is actually the better course of action: First, it protect you in case something does happen. You never know the creativity of people – someone, somewhere might figure out how to die from an unregistered chat client.
More importantly, it puts the issue on the agenda and parliament will have mercy with you and update the law soon(ish). And that's actually quite important, because while it may seem innocuous to ignore a stupid law in a case like this, you don't want that practice to spread. The rule of law is pretty important – and I'm not speaking of dictatorships here, but simply knowing, as a citizen, what to expect from your interactions with the bureaucracy.
Example: Should I buy that open lot downtown and build a house? Well the law says it can't be build because it's too close to the river, but I've heard they usually disregard that law because with the new dam upstream the river no longer floods... -> Legal uncertainty is poisonous for any development.
> More importantly, it puts the issue on the agenda and parliament will have mercy with you and update the law soon(ish)
Complicated motivations like those don't hold up against Occam's razor. Also, the Telekommunikationsgesetz has been updated multiple times since the 90s. Suffice to say that no one should expect any improvements. Each change was a combination of very bad and very stupid ideas, with some minor improvements, which subsequently got removed before the changes were passed.
Sometimes it's even scarier when they do and discover what great capabilities for surveillance and control it can offer.
But, to be fair, Germany was always crazy like this. There was always censorship of media (trying to have developers registered stems from that), that goes back to when Germany was a collection of small kingdoms. Add the conversative mentality of its people (when book printing was invented, they decried the harmful habit of reading too much) and you have to end up with that backwards, crazy and megalomaniac little country Germany is today.
And I speak here as German.