How to run KNN (or other) on nested features? Image metadata
You could try to apply a dimension reduction technique to map all of the variables into 2, such as t-SNE or UMAP (I recommend this one), and then apply a clustering algorithm based on densities, such as HDBSCAN.

Be mind that each run of the HDBSCAN might return different results.
Scale all the variables before starting to apply the algorithms (scale)

Links to these algorithms in R: 
UMAP: 
HDBSCAN