"Likely" is an adjective. It qualifies the dummy "it" in the first option.
In the second, you're using "likely" as an adverb. While it can be used as an adverb, that isn't the correct structure for it to be used as an adverb. It's not said that way. Sometimes the reason a structure is wrong is that it's just not used, as in this case.
It will happen.
How likely is it?
That amounts to How likely is it that it will happen?