At the risk of confusing things even more....my understanding is that deinterlace is usually only needed with old material like tv shows or animations that are interlaced videos. (You will see a tooth-like pattern coming off of edges in the video). The act of deinterlacinging adds a lot of time to the transcoding.
However, you can set Handbrake to Decomb with a "default" setting let HB determine if deinterlacining is needed. Therefore, if you leave it at it's current High Profile setting of Deinterlace/Decomb (default), it will have no impact on the transcoding time or quality. It only kicks in for a few rare occasions (mentioned above). Or, if you are sure that your material is not interlaced, you can turn it off, again with no impact. So if it has know impact on anything (unless HB determines it is needed), why not just leave it on, right?