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It's a good point to make, but people tend to immediately go into defense mode because they don't want to live in a world that possibly couldn't be captured by finite/human means.
Yes, e.g. if the notion of particle (electron say) is fundamental and "real", then, if each and ever particle would be in fact governed by their own completely independent laws of motion, then we would have a hard time finding this out and, generally, there's no way to rule that out.
One resolution is to give up the idea of "knowledge" and approach the situation from an effective/practical view point: Our theories are simple because more complicated theories (more parameters, more non-linearities, more abstractions) would just not be helpful to humans.
E.g. human physicists are "desperate" to explain everything in terms of "energy conservation" because it was a successful strategy for model building previously and mathematical systems with those properties are integrable. I.e. fixing quantities, e.g. introduced by postulating symmetries, means you can integrate out degrees of freedoms and your physical models are thus actually able to enable computations.
We use simple theories because hard theories wouldn't be of any use - but yes, to then go on and take up the viewpoint that this would imply that the universe itself is actually describable, on a fundamental level, by such simple theories is, as they say, cope.
