Also, perhaps more importantly, if the meaning were 'they were not at school' estar would be used instead of ser, because the state of being or not being at school is temporary. ie ellos no estuvieron en la escuela hoy. Fui/fuiste/fue etc. are mostly only used as was/were to describe characteristics (it was nice) or dead people (he was a teacher) - not locations.
The use of articles is hard to comprehend for English speakers. Sometimes Spanish uses articles where English does not and vice versa. It isn't just that "suddenly it's acceptable". The article should be translated when it is correct to do so, and should not be translated when it is incorrect to do so. In this case ("la escuela), the article is used in Spanish but not in English.
In Spain at least ( I'm told by my daughter who lived there a year) if we are still in the time period (in this case "today") you would use the present perfect rather than the preterit: Ellos no han ido a la escuela hoy - they have not gone to school today. If it the time period was "yesterday" preterit would be correct. In Latin America however, it is acceptable to use preterit for both current time period and a period of time that is considered past. Note that being "in the time period" can be any length of time - this morning, this year, this lifetime, etc., vs. last month, last year ...