Learn Croatian: Sumnjate li na njega jer nema alibi? - Do you suspect him because he has no alibi?

It uses the verb-first question structure you are learning now. To ask a yes/no question without using Da li, you put the verb first (Sumnjate) and follow it immediately with the question particle li.

Why does it say na njega (on him) instead of just using a direct object for 'him'?

In Croatian, the verb sumnjati (to suspect) requires the preposition na followed by the accusative case. So literally, you suspect 'on someone' rather than suspecting them directly.

Could I use the short pronoun ga instead of njega here?

No, you must use njega. Prepositions like na always require the long (full) form of a pronoun. The short form ga is an enclitic and cannot be placed right after a preposition.

How does the negative verb nema work here?

It means 'he does not have'. The verb imati (to have) is special because its negative form merges the word ne with the verb itself, giving us nemam, nemaš, nema, etc., instead of keeping them as two separate words.