The pickling solution, combined with the cooking heat in the recipe will destroy the living organisms in the pickles, regardless of the pickle shape. Think of the many pickle types in the market. There are whole Gherkins, Dill spears, Sliced dills, sweet, and bread & butter varieties. You can purchase sandwich sized slices, and a host of others.
Chunking your pickles will definitely make them more of a mouthfull than processing sliced cukes. And it won't be as easy to make them into a sandwich. But nutritionally, and with reference to the safety aspect, the shape makes no difference, except that as stated above, they may need to work longer in the pickling juice, which they will as they sit on the shelf.
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