What Germany might have been roaming the Cafés is still a bit of a large topic:
Don't forget Salazar, a culturally authoritarian dictator, during and before WW2, was very much on the side of Franco, and Salazar declared Portugal neutral in WW2. He had no problem with anti-democratic Germany (Salazar took issue with the anti-catholizism of the Nazis; but, well, taking issue on a philosophical level…).
Portugal was an important trade partner for Germany, especially in terms of supplying tungsten, which was important for armor-penetrating munition, as well as rubber, necessary for anything that goes somewhere without a horse. So, there's bound to be quite a few Germans in Lisbon, Porto and industrial cities all over Portugal 1941. Mind that this trade takes the form of mining concessions; i.e., it was partially German companies that dug on Portuguese soil. It's well-documented that this upset Great Britain, but they applied extensive pressure no earlier than 1943, and only in 1944 Portugal severed diplomatic ties with Germany¹.
So, in other words, there were German salesmen, captains, miners, engineers, cooks, accountants, and their families in Lisbon, probably, at least coming through. Being one of the few European countries that traded with both the Allies and the axis forces, it's not unlikely there's been also a few grey to black market vendors for German goods there (say, machinery and replacement parts for German machinery that might have demand in GB but no legal way to import them); but that's now strictly speculation.
Other than that, Germans just tended to live quite everywhere; Germany didn't establish trade with Portugal just to wage WW2, both being seafaring nations, there's bound to be some local settlements, German gentlemen's clubs, plain Kneipen (pubs) where you'd read a German newspaper… The world war certainly posed a problem for families who just happened to live in Portugal and happened to have ties to Germany. It's pretty likely that Estado Novo wasn't a great context to have a German-culture club – but then again, Salazar's idea of a state was ultra-conservative, and nationalist, and if you could arrange with that, it might not have been an existential threat.
¹
Wheeler, Douglas L. “The Price of Neutrality: Portugal, the Wolfram Question, and World War II.” Luso-Brazilian Review, vol. 23, no. 2, 1986, pp. 97–111. JSTOR, http://www.jstor.org/stable/3513243. Accessed 27 Aug. 2023.