Currently I'm mixing manually using raw vinyl, but I'm looking to buy Traktor Scratch Pro 2 with time coded vinyls:

When I'm running through Traktor will I still be able to play raw vinyl without changing my setup?
Currently I'm mixing manually using raw vinyl, but I'm looking to buy Traktor Scratch Pro 2 with time coded vinyls:

When I'm running through Traktor will I still be able to play raw vinyl without changing my setup?
Yes.
Just change the input switch of the mixer to "phono" whenever you want to play a proper vinyl, then change it back to "line" to play the files.
Obviously you can't use the software functions on the old school vinyl (effects, cue points, loops...), you have to stick to the hardware in your setup for beatmatching, effecting and so on, but it's still fun. :)
The phono inputs have corresponding outputs, and the circuit is labelled "thru" -- so it seems to me that having the Traktor in the path will make no difference whatsoever, when using conventional records.
Native Instruments (creator of Traktor) provides a multicore cable in order to connect turntables correctly to the mixer so that the system can work properly in DVS or Analogeu mode. DVS mode is always set to line so just use the Line feed in the Mixers for DVS or Phono for analogue sound on the fly.
Multicore cables are not needed to achieve this but really do make setting the system easier and way faster than multiple cables.