It depends on your thought experiment - mathematics can be categorised as a form of thought experimentation, and it's generally helpful.

Thought experiments show you the consequences of your starting axioms. If your axioms are vague, or slightly wrong in some way, you can end up with completely ridiculous conclusions. If you are in a position to recognise that the result is ridiculous, this can help. It can help you to understand what your ideas mean.

On the other hand, it sometimes still isn't that helpful. For example, one might argue that an object can't move whilst being in the place where it is. And an object can't move whilst being in a place where it is not. Therefore an object can't move at all. I can see the conclusion's a little suspect, but working out why isn't quite as easy. (The answer is infinitesimals / derivatives, we now know). But if the silly conclusion wasn't about a subject where I could readily observe the actual behaviour, I might well accept the conclusion mistakenly.

Logic can distill all the error in a subtle mistake in your assumptions into a completely outrageous error at the end. Sometimes that property can be helpful, sometimes not.