Disabled output variables do not defuzzify.
Disabled Input variables do not activate antecedents in the rules (see https://github.com/fuzzylite/fuzzylite/blob/release/fuzzylite/src/rule/Antecedent.cpp#L72).
There are no limits on numbers of rules. Personally, I find more than 100 rules to be really hard to trace the correctness of the model. Perhaps you may want to split the model into different controllers and cascade them.