Shall I write in ink or in pencil.
Why not say:
Shall I write in ink or in a pencil?
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In this context, 'pencil', like 'ink', is a material. You can use in with materials, but it wouldn't make sense for something to be in a pencil. 'A pencil' refers to the tool, and so one uses 'with' i.e. with a pencil.
If an English person said write in a pencil, I would understand 'a pencil' to mean "a particular type or colour of the material 'pencil'". In the same way, one can 'write in an ink', but this sounds more normal than 'in a pencil'.