I am trying to decide if it will be worth going for a full bachelor's degree or work towards the certification? What are the pros and cons of doing one or the other? I do have a bachelor's from 2008 in applied studies but it has not helped me find a job in that field.
Getting a first BS degree is helpful because it shows employers you can apply yourself and you know a certain amount about a topic. Since you already have a degree, it takes care of the first part - that you can focus and follow through. Which means you just need to show you know the material now. A Java cert can help with that. So can a "certificate" from a school (which typically means 4-6 classes) concentrating in a topic.
While I don't think you need another BS, note that many schools don't make you take all 120 credits again. Rather they count some classes you already took and let you start from that point. Alternatively some schools let you take enough classes in a subject to get up to speed and go straight on to a masters. If your goal is to get another degree, it's a nice path - less classes and a more advanced degree. If your goal is to get a job in the nearer term, getting a degree isn't the way to get there.
I know I want to get my Master's degree but when I checked into the program that I'm interested in at University of Minnesota, they require a computer science degree or similar which mine isn't (equine science/business) along with a year of professional work experience. My situation is a bit more complicated than normal in that I am also deaf in both ears and have a difficult time even getting a job in a professional field since well.. you know being deaf means there's that obstacle to communication. Any suggestions?
It's too bad that your local university has those requirements. You might consider another university that recognizes your existing coursework. I'm guessing there aren't that many choices at Minnesota, but there are online accredited schools. For that matter, you could take free courses at coursera and show the generated certificates at interviews to show you've been learning more than just what the cert shows.
As far as the deaf part, employers in the United States are supposed to provide you with reasonable accommodations. I have no doubt that illegal discrimination occurs though. As far as gaining experience, can you intern or volunteer? Or do a project online at odesk or the like? (if you don't have to talk to anyone, they won't know you are deaf.) As far as actual employment, consider a government job. They should be better about not illegally discriminating.