Why is the Chapel in the Tower of London St Peter AD Vincula, not St Peter in Vinculis?

I do not know the answer, but I will take a guess.

There is a shrine in Rome called ecclesia Sancti Petri in vinculis where the chains that bound Saint Peter are kept as relics. A yearly festival in honor of Saint Peter was kept there, which (naturally enough) came to be called festum Sancti Petri ad vincula, the feast of Saint Peter "at the chains", these chains being the actual relics venerated at the shrine. This was purely a neighborhood festival at first, but it soon spread throughout Rome, and from Rome, throughout the world.

Once the feast was on the general calendar, it became possible to start naming local churches in honor of the feast. We are perhaps more familiar with this phenomenon with Mary: Our Lady of Mount Carmel is one of many feasts of Mary, and it is not unusual to find churches named Our Lady of Mount Carmel even though they are nowhere near Carmel. Likewise (if my guess is right) you should find churches named Saint Peter at the Chains, even if the church is nowhere near those ancient chains.