Thank you for the investigation!
Just some comments topic:
If you confident on exactly what functionality will be used, then you can freely shrink the installation package.
But, In the future, if you decide to make some more Marvin functionality available, or there will be future versions of JChem.NET that just requires the removed assemblies you have to repeatedly test the functionality remains intact. I I think, it might create unnecessary risks.
We are working on a Jchem.NET package that contains the jars as separate assemblies.
It will also contain all the available third party jars as assemblies too. (What the current version unfortunately not.)
The good news is the assemblies can be choosen in more details (of course with more risk).
The bad news is, the full package will be noticeably bigger.
Sadly, I don't have any suggestion how to make sure, that all the assemblies are available for the functionality the user will ever use in the shrinked package.