Here are some reasons that might have contributed:
Malta is basically a limestone archipelago, with an abundance of Globigerina
limestone that is particularly easy to process and use in construction (source). This means that temples were easy to construct, and that the re-use value of their material was relatively low.
Malta had little fertile soil, which constrained the density of population, leading to better preservation of temples.
The slow process of soil formation also meant that some of the temples were never completely covered and were known for a long time. This led to an early archaeological interest in the beginning 19th century, which might have contributed to the discovery of even more temples (source).
Some scholars speculate that visual connection between different temples might have played a role in the rituals (source).