Even though there are several recurring, easily guessable family name readings ([田中]{たなか｝、佐藤｛さとう｝、田村｛たむら｝) in Japanese, there are usually many possible readings to people's names Kanji, especially first names (良 could be あきら, りょう, まこと etc).
How do attendance checks in school classes deal with this one issue? Are students' names written in Kanji only, so that teachers have to ask the students with unusual/obscure names on how to pronounce them?
First, even native Japanese adults can correctly guess the reading of the kanji names of, say, only 90% of students, at most. Quite a few people have names (either first names or surnames) with really unpredictable readings.
How do attendance checks in school classes deal with this one issue? Are students' names written in Kanji only?
The answer is 'yes, mostly', because a class is a small and stable community (40 people at most) and everyone learns how to call one another fairly quickly. There is no true need to disambiguate the reading in such a situation, in the first place. Here's how a typical checklist used in an elementary school looks like (source):
There may be a few people with really difficult or ambiguous kanji readings, but that does not justify you always have to have hiragana alongside the kanji names throughout the school year.
But what about the beginning of each school year, when people are yet to familiarize themselves with one another? In such a case we can always use a name list with hiragana readings, which looks something like this (source):
As @Urukann pointed out, virtually all organizations (schools and companies) maintain a digital list of members with a furigana ("readings") field/column. Without the furigana field, it is even impossible to sort names alphabetically! Basically whenever kanji names need to be correctly read out aloud or sorted, we need furigana (hiragana). Unfortunately, many foreign contact book applications and such are ignorant of this fact and try to sort Japanese names based on their kanji character code, which is nearly meaningless.
Most of the time, teachers do not have to ask how to read the name of a student, because they usually have access to the list with readings. But sometimes teachers may have to ask the reading of a name directly to the students themselves, as shown in @WataruSubridge's answer. This is more true in higher educations where teachers can meet many random students.
It's like this:
Teacher: 「野田{のだ} 努{つとむ}さん。」
野田: 「はい。」
T: 「いわい 隆{たかし}さんですかね？しゅくさんですか？」(the surname reads 祝)
祝: 「はふりです。」
T: 「はふりって読むんですか。珍しい名前ですね。はふり たかしさん。」
祝: 「はい。」
This conversation has actually taken place in my twelfth grade first classroom.
Note: People with easy-to-read names don't end up in this kind of awkward conversation very often.
Still, it's often the case with me that they misread my name, especially when I hear back from business entities via a phone call, even after I filled in all the items including カナ on the inquiry forms like the picture below. They often overlook カナ when they find the names in kanji easy to read. I feel really awkward making a correction every time they mess up my name.
When you misread someone's name, do apologize.
Well I don't know about school per se, but every form I've seen so far (Foreign registration, tax, social security, subscription to various utilities...) asks you to not only write your name, but specify the pronunciation using Furigana. See for example this generic contact form:
It has a 名前{なまえ} field, split into 姓{せい} and 名｛めい｝ for family name and surname. Right below, is another 名前｛なまえ｝カナ form, also split, that you are supposed to fill with the pronunciation of your name.
Thus my guess is that you fill a similar form before the beginning of the school year, and the teachers have the pronunciation available on the attendance checklist.
I do not think that there is a generic method to guess the pronunciation of someone's name without asking for it.
