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Hi Nick
There is confusion over terminology here: the Victorian 'shot glass' was a receptacle for lead shot, in which you stored your quill pen by pushing it down into the shot. It was not a drinking vessel, unlike the modern shot glass. Much of the millefiori would have been obscured by the shot...
Regarding the large bottles that people call inklwells or perfume bottles, I doubt they were often used for either of those purposes. But if you put ink into an Old English bottle, you can still see the millefiori design, because you normally view it obliquely rather than from directly above.
Alan