My guess is the vast majority is either directly from Sicily, or shared with them. The pre-Phoenician people of both islands were the Sicanians, who came to Malta from Sicily.

In the Middle Ages, the island was settled en masse by people from Sicily, hence why family surnames are largely from southwestern Sicily (Agrigento, Caltanissetta, etc).

My guess is Maltese are 95% Sicilian if not more. They have slightly higher North African and Sub-Saharan, but not a significantly higher amount than people in Sicily.