in NLP academic paper, would it be okay to refer the "token embeddings" as "tokens"?
At least to me, it would sound strange, as I would understand tokens as the discrete textual units they are, not their assigned vectors.

I would suggest that you don't try to force nonstandard simplifications. Just say what you want, in a technically accurate way, preferably using short sentences to avoid making it difficult for the reader to follow your discourse.