An individual can have a music preference. An individual can also have music preferences. There is no difference in meaning between the two sentences that I can see.
The Corpus of Contemporary American English has 13 cites for music preference (including one preceded by their) and 16 cites for music preferences (including two preceded by their).
Here are just some cites:
The 45-year-old Los Angeles native has clear-cut music preferences, and says that he's drawn to some of the older Los Angeles punk.
One person, many preferences.
Some students may have difficulty finding connections between their personal music preferences and the music taught in school music curricula.
Many people, many preferences.
Specifically, those subjects who reported their music preference as heavy metal did not show higher anger-levels after listening to this music.
Many people, one preference each.
The teaching of multicultural music and background information concerning different cultures has not only positively affected students' music preference.
Many people, one preference each, or one collective preference of them all.
Lastly, as has been pointed out elsewhere on this page, musical preference is also used. COCA has 19 cites for the singular form and 41 for the plural, showing that it's in fact used more often than music preference. Again, here are some cites:
These results mirror perfectly the subject's musical preference, where women rated the heavy metal and classical genres equivalently, and men strongly preferred heavy metal to classical.
One subject, one preference.
Still, he concedes, "if the operation is too challenging, I won't bother with it and, anyway, it's not fair for me to hold the O.R. staff captive with my musical preferences."
One person, many preferences.
French-Canadian adolescents report that rap music is their favorite musical preference.
Many people, one preference.
And so on and so forth. You get the idea.
That being said, it might matter which usage is preferred in your immediate environment. Conventions can vary from department to department, so you might wish to check out what your peers do, consult a faculty member, ask your reviewer, look at other papers, etc. But if that isn't applicable, or if it doesn't make any difference either, just pick whatever you are comfortable with and stick with it. Make sure you're consistent.