Yes, System.loadLibrary() works from a module. The DLL must be on the filesystem though, specifically in the "lib/win-x86_64/" directory of the module (whose directory is whatever the location of the module.xml file is).
In addition to what David noted, here's the doc JBoss Modules version 1 which has details about packaging the native library as part of the JBoss module
P.S: On an unrelated note, it's good to see that the docs is no longer hosted on Confluence. It really used to take extremely long to load, plus reading the actual content, navigating etc was all cumbersome.