Yes, you can update the included version of jQuery Mobile.
Download the desired version from jquerymobile.com, and replace the files within Dreamweaver's Configuration folder. Greg Rewis wrote up a helpful blog post that details this process: http://blog.assortedgarbage.com/2011/05/updating-jquery-in-dreamweaver-cs5-5/
I haven't run into any issues with the newer stable versions (i.e. jQm 1.1.0 and jQ 1.7.1/1.7.2).
If you do, though, we'd like to hear about it: http://adobe.ly/DWBug
I have updated my Dreamweaver CS6 to jquery 1.7.2 and jquery mobile to 1.1.1. Following all the great directions in the blog post mentioned above, it updated without a hitch and corrected many bugs I found after deploying my app. One big problem remains. The new Jquery Mobile Swatches dialog which worked great in 1.6.4 and 1.0 no longer works. Any help would be greatly appreciated.