Pakistan's missile program is primarily built focusing India. Shaheen-3s were built to hit the farthest corner of India and not much needed. We might have 100s of shaheen 1 but only 10 to 20 Shaheen-3. That's my personal assessment.
I think we never procured any weapon system considering Israel. Also shaheen -3 is primarily for nuclear strike. Using it for conventional hits would be extremely expensive. As you are going to waste a millions dollar missile (almost a space rocket) on a single target and given Israel's air defence that could be intercepted.
If Israel vs Pakistan ever happened (unlikely though). Then our best chance is air launched missiles. We already have Taimur missiles (600 KM) that can be launched via JF-17s, J-10Cs. So fighter jets would be refueled over Iran and they will travel till end of Iraq and release their payload and return. This is most efficient way for sustained combat operations. We can definitely developed longer range air launched weapons with upto 1000 KM ranges and can hit Israel from even safer distance. J-35 would really help in strike missions too.
Ballistic missiles are normally used for conventional hits by country who don't have an airforce like Iran. They never invested in their airforce due to sanctions / restrictions. Now any airforce can fly over Tehran without contest. We on other hand are already spending billions of dollars on our airforce, and it gives us capability for both defense and offence.
