Is it worth getting a masters in a secondary field as part of an interdisciplinary PhD? I'm in the process of making a decision with regards to graduate school and my number one choice is an interdisciplinary PhD program in Computational Science and Engineering. On the computational side of things I'll be focusing largely on data science, but I'll be looking to apply those skills to land use modeling. So effectively I'll be doing a lot of work in environmental policy. 

My goal is to go into academia after my degree and as such I'm wondering if it would make sense to pick up a second masters in Environmental Policy as part of my coursework? Doing so would likely add a bit more time to the PhD, but would this make me more attractive as a candidate for a tenure track job afterwards given I already hold a Masters in Software Engineering?
When you are evaluated as a job candidate in academia, the first thing people will see is your PhD.  That will tell them that you know how to dig into a topic, get the background knowledge that you need in order to conduct the research you are interested in.

The next thing they will look at is your publication record.  Because of the peer review process, they will feel confident that if you publish in reputable journals on a particular topic, you know what you're talking about.

So if you're sure you're headed for academia, I think you will be fine just cherry-picking the particular courses you think will be most helpful for you in Environmental Policy.  (Although if you find that you're, say, only one or two courses away from satisfying the requirements for the masters, then I suppose you might as well finish it off.)

Think of how many PhDs veer off in a different direction during the course of their career!  They don't bother getting a new PhD in the process, because they already have one.  You can think of the PhD studies as the apprenticeship to do research, and the PhD as a driver's license which was issued in one state, but which you can use in other states.