Wow... 12 hours... somethings not right... what settings are you using... On my mac pro even with 2 pass encoding it takes approx 1.5 to 2.0 hours.
The deinterlace is something I use a lot on my old japanese films... dont know why i thought it would be a good idea to always keep it on... if its not needed youll loose 1/2 of your vertical res. bummer
Deinterlace: as has been mentioned, only deinterlace an interlaced source. Deinterlacing slows encoding excessively and also will lose quality when used on a non-interlaced source. If your not sure, then try the HB snapshot and use "Decomb" which only applies deinterlacing to interlaced sources.
Detelecine: only detelecine a telecined source.
Denoise: This one should really only be used for excessively noisy sources, like maybe live concert footage from the 80's or something, beware that it "can" cause a sort of "plastic" look to the video.
All of these filters will add to your encoding time and if used on the wrong source could degrade output quality. If you are generally encoding major motion pictures then frankly I would not use any of them with the exception of Decomb in the latest HB developer snapshot and only if your not sure if the source has any deinterlacing ( which in the macgui version of HB should show up as "jaggies" in one of the ten picture previews, not extremely common for Hollywood major motion pictures).