Could Someone help me knowing whether in.pool.ntp.org is synced with NIC or NPL server in India. or On which basis the time is synced in in.pool.ntp.org servers?
We don’t know, but you can check yourself.
Just add the pool to configs and NIC/NPL as well then check if they differ a lot.
Normally servers are within 20ms or less.
If NPL is way off, it means their time is not correct, then you have a problem as India forces companies to use timeservers that are not out of synch with NIC/NPL.
You could also use both, then your clock will be correct, even is NIC/NPL is off.
Have fun, as NTPPOOL is about correct time, would be weird if NIC/NPL is off themselves 
Welcome to the forum!
The servers are operated by volunteers, each of which can configure them however they want. If you have a regulatory requirement to sync to NIC/NPL’s servers, you should probably put their servers in your ntp.conf / chrony.conf file directly.
I have two servers in the India pool zone that are configured with NPL as a source, but it’s not currently the selected source on either of them. For example:
chronyc> sources
MS Name/IP address Stratum Poll Reach LastRx Last sample
===============================================================================
^- www.time.nplindia.org 1 10 377 316 +861us[ +861us] +/- 22ms
^+ www.time.nplindia.org 1 10 377 267 +1030us[+1030us] +/- 23ms
^+ mail.nplindia.org 1 10 377 709 +497us[ +497us] +/- 22ms
^- sgsin3-ntp-001.aaplimg.c> 2 10 377 796 +760us[ +932us] +/- 48ms
^- sgsin3-ntp-002.aaplimg.c> 2 10 377 441 +598us[ +598us] +/- 48ms
^+ ec2-15-206-210-239.ap-so> 4 10 377 846 +198us[ +369us] +/- 8594us
^+ ec2-65-0-107-254.ap-sout> 4 10 377 843 -197us[ -26us] +/- 8353us
^+ ec2-13-235-60-53.ap-sout> 4 10 377 882 +245us[ +416us] +/- 8292us
^* ec2-65-1-129-94.ap-south> 4 10 377 790 +136us[ +308us] +/- 8373us
The servers are all in pretty close agreement. I think the fact that it’s preferring Stratum 4 doesn’t mean much; it seems like Amazon runs stratum 1 through 3 all in the same data center, and then stratum 4 is an instance there, so it’s all pretty accurate. (On another server, I set up a prefer keyword to favor stratum 1 servers so I wouldn’t be a stratum 5 server, but I think I’m ultimately sacrificing accuracy to do that.)
Mine do use NPL (and the other one also has NIC), but I doubt every server in the pool does. You should probably add them to your config locally.
I also have a server in the India zone. While it currently uses the NPL-India NTP servers as a time source, this could change at any time. Any / all of the NTP Pool servers can change configurations at the operator’s whim.
I’ve had problems with the NPL-India NTP servers. A few years ago none of them was reachable for several months.
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You got to be joking!!!
No, not joking. Starting July 25, 2014 14.139.60.106/107 were unreachable for many months. I never discovered the cause.
From memory, but I think in one of the leap second years there was a country with a “national standard institute time service” that was off by a second for either several hours or several days … Computers are hard! 
Maybe they are handling leap second the OpenBSD way.
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