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Hi Miiya,

If you enter Japan on a work visa, you're free to attend school (although your employer may have something to say about your work-study time balance).
*Terminology note, I use "visa" to refer to your initial permission to enter the country. Your legal permission to stay in the country to accomplish a specific purpose is called a "status of residence."

You can also change from a work status of residence to a student status of residence once you're in Japan and have acceptance from a university.

The only complication comes into play if you're looking for scholarships. I think all of the full-ride scholarships (Monbukagakusho, etc) and most of the partial scholarships will only pay out to students who have a student status of residence.
I work in the international center at a private university here, and each month we have to make sure our Monbukagakusho scholarship recipients haven't changed their status of residence before they can receive their stipends.

If you're interested in the reverse approach, you can enter Japan as a student (with acceptance from a university), then apply for work permission. You would need approval from your university, but that should be a formality, as long as you're not failing classes over your job.
As a student with work permission, you can work a maximum of 28 hours per week and a maximum of 8 hours in a day during the long vacations. Some specific jobs are forbidden (anything related to the entertainment industry, or the "entertainment industry.")
Regarding coffee houses, I've actually seen a statement that students are forbidden from working in coffee houses where the ambient light is less than 10 lux. So, if the place is figuratively or literally shady, it's out.

Sorry, I don't have any direct experience with students working at Starbucks, so I'll have to wait for someone else to chime in.

Good luck!
-Travis from TranSenz
Find the TranSenz Blog on Expat-Blog here!

I got a work permit when I lived in Japan on a student visa (Although they cancelled my job -_- www). Don't worry too much. Just need some papers from the employer, bring them to your school and have them filled out/signed by your teachers. Then go to the address on the paper and get your permit (you need to pay a little though).