You're assuming too much

As far as I know, European pandemics like the Black Death typically killed up to half of the population in towns and cities. However, we also know that when smallpox was brought to the Americas, it killed 90% of the Native American population.

Death rates were high in both instances, you're taking very round and anecdotal figures and comparing them -- neither "up to half" nor "90%" should be take as some kind of medical census.

This is a useful example to learn from: before trying to infer something from comparisons between data, first validate the data itself. Whatever uncertainty or unreliability one might have with one data set-- when you try to make comparisons between two data sets, each with their own problems, you end up with noise^2.

So far as we can tell, no one was immune to plague, whereas smallpox infection as a child is typically not lethal, and confers longlasting -- typically lifelong-- immunity. Similarly, exposure to cowpox (and perhaps other pox viruses), will induce subsequent immunity in without a severe clinical disease. So plague and smallpox are different disease causing entities in that regard. The most devastating of the smallpox epidemics in the Americas -- and note that Europeans born and raised in the Americas who'd not been exposed to smallpox in childhood were also susceptible-- killed a large number of adults, devastating indigenous communities. This loss to disease occurred at the same time as massacres and forced dislocations, so you're talking about an epidemic occurring in a population who are often refugees-- that's a bad mix.

Plague is a remarkably nasty disease entity, and septicemic plague in particular will have a fatality rate approaching %100 without prompt treatment with modern antibiotics and other supportive care. Pneumonic plague is still devastating, "fatal in all instances unless antimicrobial treatment is started on the first day of symptoms."

What we can say about plague is that its geographically limited by its vector, rodents with fleas. . . places with more plague infected flea ridden rodents -- port cities for example -- would be more affected than places with fewer. One also finds, for reasons we only partially understand, apparent differences in the lethality of different plague events; medical historians continue to try to figure out why. Smallpox, by contrast, is transmitted person to person; it can be anyplace there are people.

So: different diseases, different immune responses, different historical conditions, different timeframes. One can find communities abandoned due to plague and communities abandoned due to smallpox and the comparison of anecdotal and inferred fatality rates doesn't tell you anything much.

Sources:

Butler, Thomas. “Plague gives surprises in the first decade of the 21st century in the United States and worldwide.” The American journal of tropical medicine and hygiene vol. 89,4 (2013): 788-93. doi:10.4269/ajtmh.13-0191

Fenn, Elizabeth. "Pox Americana: The Great Smallpox Epidemic of 1775-82" (Hill and Wang:2002)

Daniel L. Zimbler, Jay A. Schroeder, Justin L. Eddy, Wyndham W. Lathem. Early emergence of Yersinia pestis as a severe respiratory pathogen. Nature Communications, 2015; 6: 7487 DOI: 10.1038/ncomms8487