The student visa prohibits/limits you from holding employment in Japan. It doesn't explicitly prohibit you from buying and selling things for profit. Note that the tax authorities could view your profit as miscellaneous income, and depending upon how the money flows to you (and the amount) it could present some difficulties.
In general, assuming you have the rights to sell the software you are selling, there shouldn't be any issue with your visa.
I intend to pay the taxes related to this revenue here in Japan, I just don't wanna lose the scholarship. I thought it was as you say, but some people from the university administration are telling me to investigate further.
Wow - I wouldn't have expected that. Bear in mind that you can always ask for permission to engage in activities not covered by your student visa. My guess is that this would be easy to get. 法務省：資格外活動許可申請