First, there isn't a place on your car you can hide a key that someone looking for it won't find it. And if your insurance company finds that you are doing it, they may be under no obligation to cover your car in the case of theft. You have a choice as to what you do, but I would be real careful about doing this. These keys are also very expensive for a reason, the added security that the key creates. Normal keys on older cars were very limited in the number of key combinations the could really handle so the keys were duplicated even within the same model line. Usually this isn't a problem that people run into, but once in a while you will find stories of someone opening the wrong car because the key fit and they didn't notice it wasn't theirs. So if you look at keys in general that provide this facility, most are approaching this general size, in fact my Subaru key which didn't provide this function wasn't much if any smaller than the key portion of this key from a length standpoint (it was rather a bit thinner).
Next, the Honda key is more rounded than most car keys which means that it is less likely than a normal house or car key, to cause any damage in a small bump.
Finally I would bet if you check the one key model is more expensive than the key and separate fob. Ergonomically the one key approach is probably better because you can definitely use the key by feel without having to figure out which side of the fob you have, also it makes for less clutter overall.
But like several other things, people are going to have different opinions on this. I think this key is great, I have less stuff in my pocket now that it isn't a key with a separate fob as I don't have a big ring between the key and the fob anymore. It also lays flatter in my pocket than the old setup. The only way I have ever scratched a car with my keys is trying to unlock the door with the key and not knowing where the keyhole really was, but since going to remote car door openers this hasn't been an issue for me.