How about including visa-free countries in your travel options? For example, Singapore and Costa Rica are visa-free for Filipinos. If your wife is not already an international traveler, adding stamps to her passport would bolster her future visa application to Japan or South Korea.
An explanation letter is not necessary, though if you want to submit one, it wouldn't hurt. It would be clear from the visa application form that your wife is a student, she is married to a USC, you are sponsoring her, and you have a job. As supporting evidence to the guarantor info in the form, your wife should submit to the visa agency: a copy of your marriage certificate, your recent pay stubs, and your bank statements.
I was unemployed when I applied for a Japanese tourist visa, so I submitted a letter with my application. Unlike your wife, I was single, self-sponsored, and not a student. In the letter, I explained my lack of formal employment, details about my financial capacity, and the countries I visited before. I was granted a 30-day multiple-entry visa.