If or since, does it make a difference?

Yes it does.

1）Since you are unemployed, why did you leave your last job?
2）Since you are innocent, why did you flee?
3）Since you are a Christian, why do you believe in a personal God like this?

Now these all assert something to be true, where before they only assumed something might be true.

1) Does if here suggest a hypothesis, which means anyone who speaks these words is not sure or does not admit the fact?

This is true only insofar as the use of if itself does not imply the fact. It can be used in contexts where the fact has already been implied. It's in those cases that a switch to since can be considered. But that doesn't necessarily make use of if wrong.

"You say you're too busy to talk. If that's true, why are you still talking about it?"

"You say you're too busy to talk. Since that's true, why are you still talking about it?"

2) Does replacing "if" with "since" make the clause a fact rather than a hypothesis?

Yes. Since should not be used unless asserting a fact.

3) If replacing "if" with "since" does make a difference, can "if"still be used if the context can imply that the clause is indeed a fact?

Yes. If can be used independent of knowledge of fact. If can be used to indicate assumption of fact (hypothesis) or to lay out conditions used to select between options.

"If you are as short as we all know you are then you can't ride the rollercoaster"