Depending what u want. If u have a android Windows Mobile device that has a bultin scanner u should use the comport to communicate. If u want to use the camera i suggest u use one of the existing apps for scanning barcodes. (U can launch them using a intent). The downside is u need to install a second application.
More on launching a other app in WD http://www.mysnip.de/forum-archiv/thema-27131-126196/WM16+Android+-+Open+App+from+an+App+SOLVED.html