Not in my time, David. Early Communion services on Sundays, All Saints Day, Ash Wednesday and Ascension Day were optional, other services were whole school. The only exception may have been Lent Addresses which were on a Wednesday evening, it is possible the Junior Houses didn't attend, but I was never in one.
There were a very few Roman Catholics who could go to Mass in Hertford, I'm not sure of details.
We had at least one Jewish girl in the school in my time Ruth Fraenkel, better known now as Baroness Ruth Deech. I can't remember whether she attended chapel, she is several years older than me, and was in another house. Famously she did not receive a leaving Bible when she left school, I believe she was given one years later!
In my last year we had our first Muslim pupil in 6s. I know she was allowed to say her prayers separately, in a room where a Junior would not normally have been allowed, the Head of House's bedroom. At first she encouraged others to come and watch her pray, but we discouraged that!
By the way, David, my Katharine is spelt with an A after the H. My classically educated OB father said that was closer to the Classical Greek!