Learn Spanish (Latin America): ¿El niño es rebelde u obediente?

This is to prevent two "o" sounds from crashing into each other. Because obediente starts with the letter o, saying o obediente would sound like one long stuttered word. To fix this, Spanish changes the conjunction o to a u before words that start with o or ho.

Does using u instead of o change the meaning?

Not at all! u still exactly means "or". The change is strictly a pronunciation rule, much like how "a" becomes "an" before a vowel sound in English to make it easier to say.

El niño is masculine, so why don't the adjectives end in -o (like rebeldo or obediento)?

Adjectives that naturally end in the letter -e in their dictionary form are gender-neutral. You use the exact same words, rebelde and obediente, whether you are talking about a boy (el niño) or a girl (la niña).

In English we ask "Is the boy...", but the Spanish sentence starts with "¿El niño es..." (The boy is...). Is that correct for a question?

Yes! In Spanish, you do not always have to swap the subject and the verb to ask a question. You can often just take a regular statement, add question marks, and raise the pitch of your voice at the end of the sentence.