No. Flodesk does not double-count your subscribers, regardless of how many segments they are in. 

This means that if you have one subscriber on your entire list, and that single subscriber is added to three segments, you will see that each segment has one subscriber in it, but your total "All Subscribers" segment will show only the one subscriber.

We also do not send duplicate emails to subscribers, which you can read more about here.
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Additionally, since we have a flat pricing model, you'll never have to worry about how many subscribers are on your list!