The easiest way to get to the source is disabling the corresponding library (if d.ts files were downloaded as a library)/removing typescript definitions from project. Then WebStorm will try to find the definition in .js files.
There is a feature request for a possibility to 'merge' TypeScript definitions with available .js definitions, using d.ts for completion and .js - for navigation (WEB-12630). The only problem here is that WebStorm can't always find the correct definition in .js - and that's the reason for using TypeScript definitions instead. For example, if the module properties are defined by iterating files in file system:
fs.readdirSync(__dirname + '/middleware').forEach(function(filename){
if (!/\.js$/.test(filename)) return;
var name = basename(filename, '.js');
function load(){ return require('./middleware/' + name); }
exports.middleware.__defineGetter__(name, load);
exports.__defineGetter__(name, load);
});
Resolving them for completion/navigation doesn't seem to be possible