Installing the
re4son-kernel will almost double the speed and using a really fast SD card (I'm using a Sandisk Extreme Pro 32GB for my compiles) will improve it even more.
I'd also add a swap file when you are compiling stuff on it.
Please let us know how you go.
@Animesh, What sd card are you using? Are there any hints relating to your problem in the journal, something unusual during shutdown? I've been running about a dozen Pi's with Kali 24x7 for years and never had any problems. I've always been using sandisk ultra for dev and sandisk extreme pro for prod.