In the following setup:

version: typescript@1.9.0-dev.20160127

jsconfig.json

{
    "compilerOptions": {
        "module": "commonjs",
        "target": "es5"
    },
    "exclude": [
        "node_modules"
    ]
}

circle.js

const PI = Math.PI;

exports.area = function (r) {
  return PI * r * r;
};

geometry.js

const circle = require('./circle.js');
console.log( `The area of a circle of radius 4 is ${circle.area(4)}`);

Go to definition from geometry.js area works and navigates to the file circle.js.

Doing a reference search from circle.js exports.area doesn't result in any references.

When changing the code of circle.js to:

const PI = Math.PI;

export function area (r) {
  return PI * r * r;
};

then the reference search returns the correct result.