If you are in the USA, the Magnuson-Moss Warranty Act says the manufacturer cannot require that you leave the car stock or use only OEM parts or consumables. If Honda can prove that your intake caused an issue, or you caused an issue when installing it, they can refuse related warranty service. From my understanding, it is up to the warranty provider to prove that the modification was the cause of the problem.
A common example is where a vehicle owner installs a new muffler, and the transmission fails. The manufacturer would have to be able to prove, not just that the replacement could be responsible for the transmission to fail, but that it did cause the failure. (For example, the muffler fails in a way that blows hot exhaust gas directly onto the part of the transmission housing where the electronics are, and the trans failed due to the electronics overheating.)
On the other hand, if you replace the intake, and get a CEL due to a mass air flow sensor, it would be easy to say the two are related.
There is a tricky middle ground when it comes to doing things like installing or swapping out turbochargers, adjusting fuel maps, or installing aftermarket ECUs. It gets easier to blame things on major changes.