I'm a third-year computer engineering PhD student. My dissertation topic is re-configurable caches (computer architecture) and my supervisor is a very nice person. I have four publications with him in well-known conferences in my area. But currently I'm in a weird situation. In my 2nd year I fell in love with computational neuroscience and started working on it with another professor in my university simultaneously with my PhD research. Obviously my PhD supervisor encouraged me. Recently I got two high-impact journal publications as a first author on cognitive neuroscience. I am very happy with my dissertation topic but also want to include my neuroscience papers in my résumé. I would like to try for faculty positions after the PhD. Do you think my résumé can create confusion among potential recruiters or will it show multidisciplinary research interests?
The only real danger you will have with prospective employers (presuming that you look for a postdoc before your faculty search) is that a potential advisor might be concerned that if you aren't engrossed in their research, you will seek out opportunities in other areas. If it's their money that's supporting your time, then you'd be expected to devote your effort to the line of research you've been hired to do, not what you'd like to do.
This is something that you'd have to explain in your cover letter in any case. But you'll need to explain—as you have—that your lateral move was encouraged and done with the support of your current advisor. Otherwise, it could be a concern.
I am in a similar situation (atmospheric physics and education), I was advised to include them all in my resume. A caveat that I was give is that the majority of papers be in the area that you wish to pursue as a career, but by writing in 2 areas, this can open up more opportunities for you.
The reason I was given was that all the papers demonstrate, as you have said in your question, strong interdisciplinary research skills. Additionally, all papers show that you are capable of writing research that contributes something new - with this, it does not necessarily matter that they are from different disciplines.
I strongly agree with the latter. I am in a similar situation right now (change of plans regarding my Ph.D topic, even field if you like),I was strongly encouraged by my supervisors to publish a journal paper in my previous field (which I did eventually). I can understand your fear of having an impression of jack of all trades-master of none, but if you've managed to publish good papers in both fields, it actually shows you've mastered (or in the process of mastering) both, which in turn means you can conduct your research in an independent manner and contribute to existing knowledge. I reckon academics as well as industrial parties would acknowledge this fact if you include that in your CV.
I would disagree with one premise that underlies your question and state flatly and unequivocally that it doesn't matter one bit what most employers may think. Whether you choose to go deep in one research area or publish widely is something you can resolve by looking at what you want to do in life and weighing your current opportunities to make the most of them.
- Why would you care about any employer that is so confused about your studies that they don't take the time to understand deeply your unique talents as someone who delayed entering the workforce to complete a PhD?
Now, you might have some soul searching to do to figure out why you are choosing to frame this current research time allocation dilemma in terms of nebulous "future employer" impressions, but try to look closer to now as opposed to what you think might look superficially good to others but ultimately not reinforce who you wish to become. If you have identified a small set of high likelihood employers and they generally prefer breadth or depth, then now you have an interesting question if you want to maximize your chances with this narrow set of employers.
In the end, only you can decide if ruling out some employers due to their views is a feature or a bug in your plans for your degree.