Yes. OFF rules still count.
If the limit is 5 and you already have 5 rules created—even if some are disabled—you won’t be able to create a new one until you remove an existing rule.
Example
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You have 3 rules ON + 2 rules OFF = 5 total rules

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Result: you’ve reached the limit, and ShipKit will not create the 6th rule.
It is not possible to create the 6th rule