Hello @ThijsS.
I believe this is the behavior you are looking for is the default behavior of this filter.
I tried this in my environment with the Incident Type dynamic lookup set filter on the "Customer Service - My Portal - Cases List"
Entity List. The filter only display the Incident Types that are related to one or more cases in the list.
This is the complete list of Incident Types in my environment:
I created two Cases with two different Incident Types - and related the cases to my account and my contact.
With an advanced find I can see that there is only two Incident Types related to Cases:

Result:

Now this is how filter configuration looks like on my entity list:

And when I open my entity list I see ONLY the two Incident Types related to my cases in the filter:

I had to create a new Entity Permission for Incident Type as a CHILD permission to the Case entity permission to get the filter options visible in my portal:

Maybe you have entity permission set to widely for the filter entity?
Please try to recreate this filter using another entity with less data and see if you can recreate the behavior.
Hope this was helpful!
Good luck and all the best,
Ulrikke