As thompsonl said, you can’t simply run a deinterlacer on your NTSC footage, there are a lot of factors to take into account. The simple difference between true interlaced and telecine sources means that you need an advanced understanding of those things and cannot streamline it to a simple “deinterlace” checkbox or something.
I would suggest looking at AviSynth and its various plugins, since everything is free. QTGMC for pure interlaced material, and TIVTC + TDecimate for telecine content. Hybrid video should usually be encoded VFR.
I stand by what I said though. The ability to load an AviSynth script in VEAI would be a big leap and could achieve what you want. You would still need knowledge of AviSynth and its filters, but you would get a better handling of those things than software like Handbrake provide, without having to encode your video before sending it to VEAI.
