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You can have item categories that have different number of segments. Consider the following example that gives an overview of category setup.
Marketing wants to classify the items by the country they are sold in. (e.g. US, India, Japan)
Purchasing wants to classify the items by the commodity code and sub-code. The commodity codes are Paper, Plastic and Metal. The corresponding sub-codes are
Paper > Thick Paper, Thin Paper
Plastic > Rasin, Styro
Metal > Copper, Aluminum
So for the marketing structure, you need categories with 1 segment.
For purchasing, you need 2 segments.
So you create 2 structures under the Category flexfield.
Marketing structure one has 1 segment; Purchasing has 2.
You also create appropriate value sets and assign them to the segments for each structure.
Then you go to Item Category Codes screen and create new categories for these 2 structures.
Then you define 2 category sets - Marketing and Purchasing.
Hope this answers your question,