Yes, those are the functions of the classifier "cơn".
But I don't understand much about your sentence: Hôn cơn mưa của các hoa. Did you translate it from an English sentence? Can you give me the original?
I wanted to find how to say a similar phrase, perhaps to use in a poem, so I thought about the flowers and the drops of water on them in the morning, after the rain. Still I am not a native English speaker, I tried to translate "Kiss the rain of the flowers" or "Kiss the rain on the flowers". I think these sentences can be also metaphorical, but then I think I should not use this classifier.
Actually we have classifiers for drops of water. They are "giọt" and "hạt" and can be used interchangeably. So you can say "một giọt/hạt mưa" - a drop of rain or "những giọt/hạt nước" - drops of water, etc.