Yes we have. This was neve rthe practice of the early Christian Church. I believe this discipline cam einto being to reduce profanation of the Sacrament. It became more than that however. Part of me thinks when I serve that I shouldn’t be touching the sacred vessels, another part of me thinks it’s ok. I’ve realized that the altar server does serve at the Altar of Sacrifice. The server is the assistant to the Sacrifice. Bringing the sacred vessels can be seen as the server bringing the instruments of sacrifice to the altar. So long as there is no profanation by the server, that they don’t think it is only a cup and bowl, I see no issue. I treat the chalice with great dignity. But yes, this custom has been done away with.
I take it that you are talking about a Mass with only the Priest and a minister:
GIRM:
Sorry for not adding this before. But please note: This means that there is basically 1 person there for Mass besides the Priest. Also note: This shows the difference. Using the rubrics for Mass with only one Minister is a very rare occasion. In my over a decade of altar serving, I have only done this once.
I know that at daily Masses, things may be set up differently, however, if there are people in the pews, nothing is to be on the altar expect for what I mentioned before. This is my belief and interpretation. I am simply a lay person with no schooling in Liturgy, so take this all at face value, but I am certain many Priests would agree.
Pax!