1. You said: "It will consider as absent, if company did not receive any notification before working hours"
What will happen if he informed before working hours saying "I am not coming to work today"?
2. Since he is not covered by the Employment Act, your calculation may be OK.
3. In my opinion, that Pengesahan is not MC unless he was given sick leave for that day.
4. It is not against the law as the total hours per week did not exceed 48.
5. It depends on your company policy whether to take it as half day or full day. Make it clear to the staff.
6. Do you honestly think you should refund them?