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Your mention of Catholic archives suggests that there was an Italian community on Santorini in the I8th century. I know that the Island was once under Venetian control, but that was much earlier. I don't know, perhaps there was a Venetian community that survived after the Island passed from Venetian rule. If so, perhaps your ancestor was a merchant trading between Italy and the Greek islands of the Aegean, or even with the Ottoman Empire.
Niceta looks like it might have originated in the Greek name Aniketas, though in a form familiar to Italians.