There is clearly an issue in RDKit nodes when substructure searching with H-saturated structures which are not converted to SMARTS. See attached workflow.
RDKit Substructure Issue.knwf (25.6 KB)
RDKit simply ignores explicit Hs at least at some if not all position when query is not SMARTS. In comparison indigo does it as expected.
It seems that how aromatic bonds are drawn matters for the search results. (also see workflow). If they are drawn differently, then the structures do not match (unless Aromatizer node is used at least on the query molecule).
So if the queries come from say an sdf reader and never is converted to RDKit molecule (and /or SMARTS), then one will get confusing search results. The first issue will lead to too many results while the second one leads to too few results.
For me Indigo does it right here as it handles all the potential problems inside the search node. Works with H-saturated sdf queries as without aromatizing explicitly.
I think this is really important as results from such searches can miss important molecules.