I actually started a thread about Godel's Incompleteness theorem and its applicability to physics a few days ago, you may want to read it to see if it answers your question:
https://www.physicsforums.com/showthread.php?t=583692
Anyway, Godel's theorem certainly does not apply in general. In fact, Godel also proved Godel's Completeness Theorem, which basically shows that in a first order logic, all true statements can be proved from the axioms, and thus the true statements in a first-order logic are in fact enumerable (I hesitate to say countable since I don't want to sneak in any mathematical logic). In other words, you can't "Godelize" a formal system of logic without introducing the Peano axioms of number theory, or some other axioms.
Godel's theorem is not a very general statement at all: Godel's proof is merely a construction of a non-provable but also true statement--he just disproves the general idea that "all truths are provable" by demonstrating a counterexample. Another nice example of a proof like this is Cantor's diagonal slash: He provides a proof that real numbers are uncountable by taking an arbitrary countable collection and constructing an additional real number not in the collection, so he proved that there are at least two different infinities, countable and uncountable. To this day, nobody knows whether there are any infinities between these two--this is known as the Continuum Hypothesis.