I noticed a license plate with hiragana characters written on it instead of Kanji. I had assumed that all prefecture names would be written in Kanji. Thank you.
No prefecture names are written in Hiragana officially. As you note they are all written in Kanji.
License plates are not from the prefecture but designated cities (some of which ARE written in hiragana (usually due a dispute about what the name a newly formed city after a merger, e.g. さいたま市))
For scooter liscence plates, any city/ward/village/town can issue them so the city/ward/village/town name appears. If that happens to be Hiragana then hiragana is displayed on the plate.
License plates in Japan are issued by a few designated cities in each prefecture, and not the prefecture itself. So the name written on the license plate is the name of the city. In a few cases (Naniwa, Tsukuba, Tochigi, and Saitama are the ones I know about) the city's name is officially written in hiragana. Because the city's name is hiragana, it is on the license plate as hiragana. Why a city's name is hiragana changes from city to city and would probably be better as a different question.