Where there are two Yosef ben Shimon in one area, there is a solution to the confusion by including the next generation up in the name, such as Yosef ben Shimon ben Yaakov; Yosef ben Shimon ben Chaim.
What if both are gerim?
This seemingly strange situation happened in my shul recently. Despite the fact that it is a small shul, there are two gerim there, with the same name (single name) ben Avraham. I'm not sure why it never happened before, but recently one was called to the Torah and both showed up.
Clearly another generation up would not help here; how could one distinguish, either for a get or in the situation described?
When there are two people with the same name they must both be present at the time of the Get. According to Tosfos, this will not be sufficient according to Rebbi Meir and one must write some distinguishing characteristic, such as a nickname or a physical trait (see Even Ha'ezer 136:5)
And for an aliya? Just gesture?
I guess that would be enough.