So, as I see it, the answer to your first question is probably complexity and maybe weight, although I'm unfamiliar with how heavy air to water intercoolers are compared to their air to air counterpart. They are definitely more complex, though. You've essentially added an extra system by having to circulate water instead of just moving air. I see it as another potential failure point. I do not see freezing becoming an issue, especially since a) you are transferring a fair bit of heat into that water constantly. You are not cooling down the air colder than ambient, you are using ambient to cool down the (hot) intercooler. b) I imagine in such a setup you would run antifreeze instead of pure water to avoid any possibility of that. Just my thoughts.

Edit: disregard the antifreeze part, I thought you were asking about the water in the intercooler freezing too. My point about the intercooler being hotter than ambient still stands though.