Well, what we can say is that there are no poisonous snake on Malta today. Today Malta is a densely populated island. During the time St. Paul would have been shipwrecked it would have been mostly uninhabited areas. So we can’t say for sure what kind of wildlife was on the island 2000 years ago before human civilization began to impact the environment. Its possible that there was a small population of poisonous snakes that were eradicated by the changes in environment that humans produced.
The other issue is that boats bring in non-native species that stow away in cargo. Its entirely possible that the snake that bit St. Paul was not native to the island of Malta but was brought there by ships and was known by people to be poisonous. The possibility that ships had accidentally and occasionally brought known poisonous snakes to the island is not unreasonable.