It's important to realise that these lines are entirely written in non-standard grammar. You could call it 'dialect' if you wish. In standard 'correct' grammar, this would be "Those who have shall have". It is very common to use non-standard grammar in song lyrics, and it's particularly appropriate here. It shows that the speaker considers herself or himself to be representing the underprivileged and the sections of society who are oppressed, marginalised or discriminated against. In this case, the use of the the language of 'the common people', language which is often stigmatised for being 'uneducated' is deliberate, and it's perfect.

It means "those that have it will win, those who dont have it (faith) will lose".

First of all, it's a poem. Secondly, it represents how a subset of a population group in the UK and possible the USA speak, or used to speak. 'Them that has got' is simply representative of how that group speaks. It is not representative of correct grammar. It refers to a parable from the Bible called the Ten Talents. (It is actually where we get our English word 'talent' from) You can look it up on the internet: Luke 19:12 - 27. It does not give the explanation - you are meant to understand for yourself. Here, there are layers of meaning.