Filters have nothing to do with the anamorphic adapter, just to be clear.
You can get filters with threads that will screw onto the front of your lens...I don't remember what the exact filter size is...72mm?
You can also get a matte box that has slots to hold square filters in front of the lens. Go to B&H and search for matte boxes, or do a search on this site for matte boxes and I'm sure you'll find a number of specific products.
Chrosziel and Century matteboxes have 2 4x4 filter slots. One of those is rotateable so you can use a polarizer if need be. You could try to stack screw-on filters but you might get vignetting. One thing to remember is that the camera had built-in ND filters so you could possibly have as many as three filters on camera at once.
Removing the lens hood is no big deal. Just unthread the knob until it stops, give the hood a ccw twist and presto!