1st and 3rd are completely the same, missing out “that” makes no difference at all. 2nd sentence can be interpreted differently from 1st and 3rd if you really wanted it to, but in the end it’s still the same - the number was not theirs. for example: your friend is playing lottery! their number is 23(you know it). you’re the one to pick the winning number from the hat. you reach out and grab a random piece of paper from the hat, open it up and the number is ...32! you look at your friend and say: “I thought that it would be your number...” meaning that you wished it was their number that your picked, but it wasn’t. you’re sad. they’re sad. everybody’s sad. if you say: “I thought it was your number” it would mean that you saw the number 32 and thought about your friend’s number (that is 23 ) and for a second thought they won the lottery. your friend is sad, your reaction is unidentified.

I thought that it would be your number. Context: You actually believed that your friend's number would appear, or be chosen, you might be dissappointed and then say this. I thought it was your number. Context: You might have made a mistake and then you would say this because the number that actually appeared was wrong. I thoight it would be your number. Context: Same as the first one above. However, If the emphasis was on "I THOUGHT" it would be your number then there might be a different context, Your friend's number DID appear and you were proven right in predicting this.