Contrary to popular opinion, the “Language of Flowers” is not and never has been a full language. There is no grammar, nor form, nor even consensus on the meanings of different flowers (often there were multiple conventions within the same city).
Definitions were determined by popular fashion among the elite (though mythic appearances and medicinal associations influence these determinations). If anything, I would argue that the exchange of flower arrangements was more akin to swapping online memes than holding anything resembling a conversation.
However, In Nomine exists in a world that is in many ways defined by human belief and mental associations. Just because bouquets and other flower arrangements fall short of explicit conversation does not mean that they need to in your game.
The Artistry skill specifically states that it can be used to read the emotions of the creator (and interpret their messages). It’s only a little hop further to say that those who are appropriately trained could make use of an artistic medium to communicate – and given Novalis’ strong connection with Flowers, it would make for the perfect “secret language” among her flowers.
I put secret language in quotes because any language developed by Novalis would almost certainly be a dialect of the heavenly tongue. A human might require an attunement (or equivalent) before they could truly speak the language, but any angel or demon ought to be able to with the appropriate language skill.
Of course, those who use such knowledge to harm nature or interfere with Novalis’ plans are likely to get a visit from some of her forms. It is still her language. Only a fool would attempt to use flowers against Novalis.
NOTE: If you do intend to incorporate the Language of Flowers into your game, I would still encourage you and your players to start with one of the real languages of flowers (even if they are unequal to the task we’re setting them). Regrettably, I did not think to copy down the author’s name before lending out my preferred dictionary of flowers – and given how many books have been titled “The Language of Flowers,” I despair at ever finding it again.