When I have used the RDKit Salt Stripper on KNIME 2.12, I have occassionally had it where the node causes the whole of KNIME to completely quit without warning.
The situation I have had this happen is on our internal cpds where Mw is in the 5,000 to 10,000 range. Of course the salt stripper probably isnt designed for such large molecules, and it was an accident I processed these large structures, but thought I would make you aware of the bug. I am not in a position to try this out on KNIME 3 or later yet, so I cannot confirm if the issue is still present.
You're right that the salt stripper isn't designed for such monsters, but it still shouldn't crash KNIME.
It could be either a memory problem or something deeper. I can't reproduce it with simple examples.
One thing you could try as a quick test case is to try running a molecule with a single [Cl-] and then a large number of carbons. This will probe the abillity to handle large (in terms of number of atoms) molecules. An example workflow is attached. If this causes crashes we know it's memory, otherwise it could be more complex and will be tricky to track down without seeing your actual molecules (which I assume is impossible).