Double CD4017 leds driver 555 clock
1) indeed, if you run the LEDs on a small current such that the ratings of the left 4017 are not exceeded, you could remove those 9 emitter followers.

2) according to the datasheet (the one from Texas Instruments) output 0 (pin 3) is high even when in reset. Only after a clock will it go low.
Look at the timing diagram in the datasheet and all will be clear (I hope).

3) it is in series with a input (RESET, pin 15) and as this is CMOS logic and I see no capacitor that could lift a voltage above the supply (near this pin) I would say: you don't need the 3.3 k resistor.

4) Yes you can use almost any oscillator or clock generator instead of the 555. The 4017 will indeed be capable to keep up up to a few MHz. But the LEDs would blink so fast that they would all light up. The idea is that the clock is only a couple of Hz which you can easily do with any micro.