Hi Phoenix26,
congratulations on your baby boy.
Until it is time for your son to go to school there will be not much of a difference apart from the fact that he will have to pay higher fees if he has to go to the poly clinic. If you go to a private doctor then there will be no difference.
School will be an issue in the sense that it will be harder for him to get into a school of choice and it will be more costly for you as you will have to pay a fee of some sort (sorry don't know the details too well).
This will be the case in primary and secondary school as well as JC. Should he wish to study at a local uni he will also find it much harder to be accepted in the uni and course of his choice. All this will not be an issue though if you're planning to send him to a private school though (Aussie, French, German, there are plenty). I don't actually know for how long you can get a LTSVP for him but once he is in school you can get a student pass for him without problems.
The advantage of all this is clearly that he will not spend 2 years of his life doing national service.
Once he is out of uni and or looking for work there will be the tricky question of what next. LTSVP will not allow him to work most likely and you don't know whether it will still be that easy to get a employment pass or PR in 20 plus years.
So the basic decision is take more risk and hope for everything to go smooth and take less risk but spend two years of his life doing NS:
a. PR and and lots of benefits + certainty that he can stay in Singapore BUT 2 years of NS
b. not PR, missing out on some benefits and a bit of uncertainty but therefor two years of NS.
Also keep in mind that NS might only be 9 mths like in many western countries or might be completely abolished in 20 years down the road. It is a tough decision I wouldn't want to have to make.
Another thing to bare in mind that he can always renounce his PR. The only consequence is that he would not have the best chances to become PR or move back to Singapore again. So it also depends what passport he is on...