Pour juice from the can into a small saucepan, holding back the cherries. Transfer the cherries to a cutting board and halve or quarter if large. Add cherries to the saucepan and bring to a boil. Reduce heat and simmer, stirring occasionally, until cherries have begun to break down and sauce has reduced in volume, about 15 minutes. Stir in vanilla and black pepper and let cool to room temperature; then chill at least 2 hours and up to overnight (this step can be done in advance).
In a large bowl, whisk yogurt until smooth. Whisk in honey, if desired. Spoon about ¼ cup of yogurt into the bottom of each of four glasses. Dollop about a tablespoon of cherries with juice over the yogurt and sprinkle with a tablespoon of pistachios. Repeat the process with another layer, using the remaining yogurt, cherries, and pistachios. Drizzle parfaits with any remaining cherry juice. Serve immediately, or chill up to overnight. (If not serving right away, do not sprinkle pistachios over the top until you are ready to serve.)