How to make filter knobs/fx knobs on ddj-t1 flash like on djm-800?

You'd have to ask Native Instruments to implement that.

If you search youtube with "flashing lights pioneer ddj t1" you should find a video that teachs you how to make the master light on the controller and then a bit more complicated the fx select buttons (the ones above your channel fader that tell you whether or not you have fx 1 or 2 assigned to that channel) flash with the beat. If you can follow how he shows you how to set up the MIDI controlls you may find your solution there. BE SURE TO WRITE DOWN THE STEPS. If you don't like the result you need to change everything and delete everything you've added to get the controller lights to work proper form factory again.

As far as I know, there is no a feature in Traktor for this purpose. Unfortunately there is no a function that can make an LED blink when we want.

In this Youtube video, the guy suggests an option using the "beat", but is not exactly what you want. Only the DDJ-S1 is that FX has LED that flashes when the effect is on and when off, the LED is lighted. It is a peculiarity of SERATO ITCH.

It's my understanding that Traktor 2.5 will make this significantly easier to achieve.