In my opinion, there's a shortage of jobs period. As a physics major, you're schooling and is impressive but the scope of jobs to which you can apply is relatively limited. In a small market, limiting your eligible job opportunities obviously just makes getting a job more difficult.
That having been said, there aren't many non-limiting Master's degrees in the sciences. There's a delicate balance between specializing and becoming limited or getting a degree in something general to the point where your skills are more broad, and unfortunately thus more superficial. With a degree in physics myself, I have found that I have had the most luck with jobs when I had some experience in the area. For instance, I did a few years research in visual neuroscience as it relates to computer vision - a more bioengineering based project. Soon thereafter, I was a researcher for an Ophthalmology department and my projects shared similarities with my pursuit in visual neuroscience.
My bottom line though would be that if you're interested then do it. It doesn't really matter what the job market is. If you find the job market is tough, you'll diversify the job types to which you apply. You'll have a foot in the door because you're impressive on paper. The only problem will be selling yourself (your ability to learn, problem solve, statistical and mathematical prowess, project oriented mindset, etc.) over those applicants who have direct and applicable backgrounds to that position. At the end of the day, you'll fall into where you want to be as long as you yourself don't become complacent.
Best of luck!