I was just thinking of this!
My dad has two brothers named William. One from each of his parents' second marriages.
The families themselves don't mingle, so I think when he is talking about one brother the family understands who it is. But for HIS immediate family (us kids), we always are like nerdy-Uncle Will, or mean-Uncle Will (family joke, LOL)?, and it does at times get confusing. I have asked him if it was weird and he doesn't seem to think it was growing up, the two brothers lived in separate states with their own lives and he rarely spoke about the one to the other.
Now that we are all older, we usually just ask how Uncle Will is and we find out about both ;-)
I personally named my youngest with a middle name that my family uses for short quite often, and found out that my oldest son's father used the same name for his new baby. It confuses my mother, grandmother, siblings, etc, but my husband and I don't use the name. I think for my oldest son it would be confusing if both his brothers had the same name. Just today he was telling me their names and it would probably throw him off a little. He's only four though, so as he got older it'd probably get easier.
Food for thought, anyways!