I think it was the episode where Emiya learns about the marks, you see Rin with only one mark and Emiya comments about it. so yea, i also wanna know why!

about the weapons, I don't think Saber's is meant to be invisible. I think its a fluke cuz Emiya is not a good magician. and Rider, I think its part of its abilities. (or maybe all of them can make their weapons invisible, which is not THAT useful in their fights as Lancer was keeping up with Saber)