Ok, let suppose Pakistan has toasted India, and Indian restore to its last and only option.
You have answered your own question. Once India is toast, should we care if there is some risk in flying over Indian territory?
Lastly, I am not privy to deployment plans of Indian subs. They do not need to be only in Bay of Bengal. They can also be anywhere in Arabian sea as well. Try looking for a submarine in large part of Arabian Sea. Last time, IIRC, they tried to look for remains of MH-370 in some parts of the sea and even combined effort of a number of nations failed to locate it in the ocean. Oceans are huge.
Now with only 4 missiles per sub, India will need several dozen nuclear subs to cause any major damage to Pakistan and still hope every missile reach it's target as intended.
Islamabad, Karachi, Lahore, Multan. Four cities can be hit with current capabilities.
Plus India is already in the process of building more SSBN. Arihant was the first ship of the class. One more Arindam is under development and is said to carry eight K-4s. 12 such missiles can do a great damage. Total planned boats are around 4. So we have 28 missiles for Pakistan.
For china, India is preparing a follow on development on K-4 called K-5. It should be having 5000 KM range.
hundreds of Air Force jet would be at disposal to fly above 750 km mark both as maritime patrol and with AMRAAM to shoot down any missile in it initial stage of launch before it picks up speed.
Boost phase of a missile lasts 3-4 minutes maximum. I doubt that much time will be enough to locate the missile and guide your aircrafts near to missile. Remember, the missile is accelerating all this time. Also it is going up, how long it will remain with in service ceiling of a fixed wing aircraft? Not enough to intercept it.
Now you are telling me, K-4 SLBM on made in India INS alone will not only successful fly over India 95% of the time but will also not overshoot into Iran or Afghanistan at your mentioned speed of MACH 35.
Well, it is called accuracy of the missile and one of the parameters in development of the missile. The reason why India has to do so many tests is to essentially rule this out. Even after being deployed and produced, there are random tests. And relax, its not just India - other