Should I mention that I am interested in developing bioinformatics tools in my SOP for a "Software Development/Engineering" Master's program?
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.