Should I mention that I am interested in developing bioinformatics tools in my SOP for a "Software Development/Engineering" Master's program? The program I am applying for is "Software Engineering/Development" master's program, I am really interested in this field of study, and I have already mentioned in my SOP that I wish to follow the studies up with a PhD and then want to have a career as a professional programmer. With all that being said, is there any need to give specific examples of what I can and want to potentially do when I become a programming expert? For example, developing bioinformatics tools really amazes me, should I mention that just as an example of what I would like to do during my career as a programmer?
Put yourself into the shoes of who should decide to select you or other applicants for this program. 
Will she/he be interested of what you are going to do after the Master program?

Also, if you really like bioinformatics, probably you should approach it more from scientist point of view than a software developer point of view. 
You should already have a strong base on biology, molecular biology, genetics and proteomics to start to develop new algorithms that give a substantial contribution in the field.