I tried a filter behind the pinhole of my Zone Zero 6x6 and every bit of dust and scratches appeared in the print, a little fuzzy but there none the less. This might ad to the aura of the image, depending on what you are after.
Just my experience with this.
gene
My experience with dust etc. using pinhole has been so bad for this reason that I decided that it simply isn't worth it. I was supposed to contribute an article about using filters with pinhole. I declined for that reason.
The only way I could think it would work alright would be to use a heavily died gelatin and actually fill the hole with it.
I just thought of another way, though. Using long exposures, you could keep the filter in motion for the duration of the exposure.
Keeping the filter clean as has been suggested, and the idea of putting the filter right up against the hole are very good ideas. In my experiments, it was impossible for me to keep the filter clean, working out in the desert in Eastern Washington with the wind blowing.
If you were to use the filter right up against the pinhole, it might not produce the noted anomalies if the filter were taped inside. Worth trying.