Hello Sony,
Firstly thank you for your question. It is a very good question. The usage between "apa" and "apakah" in Bahasa Indonesia is often overlapping. But in terms of context, "apakah" is used more in formal context or situation, and it is used in text book and formal lesson (for example in exam materials). Meanwhile "apa" is used widely among Indonesians to ask a question (generally) and it is used a lot in daily life.