Every dice site has a house edge, that's how they make their money.
And yes it effects the odds. If there was no house edge you would get paid 2x on a 50% chance to win, because that is what is fair. If we flip a coin, it's fair for heads I give you 1 dollar, tails you give me 1 dollar. That is a fair game.
Casino games are not fair, they all translate into, flip a coin, if it lands on heads, you give me $1, if it lands on tails, I'll give you 95 cents (or something to that effect). That is the house edge.