Just a few words of clarification. I am no lawyer, but even me I see some confusion here.
Trademark: NO the logo has not been registered as a trademark / service mark to the best of my knowledge; or at least ISRG is not saying so. YES it can be argued that it is actually used as a trademark, although that determination will have to be done by a court; it is not automatic.
Copyright: YES most likely the logo (padlock) can be protected by copyright. NO it does not mean that nobody can use it, because various jurisdictions may exempt certain uses from copyright protection. Under the United States law, for instance, a doctrine of FAIR USE allows usage of copyrighted material for a closed set of purposes - like, in order to identify the Let’s Encrypt service. Similarly, other legal systems based on Common Law have a doctrine known as FAIR DEALING. However, YES the permission might be needed if the logo is used in a commercial product, because these exemptions often do not apply to commercial usage.
Copyright - further: it can also be argued that the logo is in fact too simple to be copyrighted. The padlock is actually an outline of a common object and similar images have long been found in many places (including many fonts). The “Let’s Encrypt” text alone cannot be copyrighted. So, this particular logo is rather a borderline case and various jurisdictions might view potential protection differently.
Consequently, on top of asking ISRG, it makes good sense to consult a legal professional in the country where potential use of the logo is to take place.