If I create a filter that looks for a particular value in a custom field,
issues that are in a project where the custom field has been removed
will show up as matches. This is strange and annoying! Why should a filter
match if the custom field is inactive in the project settings that
the searched issue belongs to?

Another way to explain this is that the results from this SQL-query
should not be returned when you search with a custom-field filter.

select 
    i.id, p.name, concat("\"", cv.value, "\"")
from 
    issues i, projects p, custom_values cv                             
where 
    i.project_id = p.id and
    i.id = cv.customized_id and
    cv.custom_field_id not in 
        (select custom_field_id from custom_fields_projects where p.id = project_id)
order by name, custom_field_id;