First of all - relax (yes, I know it's easier said than done) but at no.134 he may well get a place at Pates in March anyway.
If he doesn't and at that time you think you'd rather he went to Pates, then you can definitely tick the box for him to be on the waiting list and/or submit an appeal without jeopardising your place elsewhere, so that takes the pressure off quite a bit.
As for an appeal, in your case you would be making an "over-subscription" appeal rather than a "non-qualification" appeal (i.e. your DS reached the pass-mark, there just weren't enough spaces.) In theory over-subscription appeals are easier to win than non-qualification appeals, but in practice it does seem that any type of appeal is pretty tricky to win at Pates, although not impossible. This is because Pates offers places for 4 classes of 30, so anyone winning an appeal has to have strong enough reasons to outweigh the disadvantage to the school and other pupils of having 31 or 32 in a class.
In theory, as your son reached the pass-mark, his suitability for Pates is not in question, so you should base your argument around why this school is particularly suited to his needs, rather than saying effectively "I know he passed, but there are reason to suppose he should have scored higher." From my own personal experience however, I feel that the mitigating circumstances I gave for my DS are what swung it for him. So you might be best advised to cover both issues. There may be things about Pates that would particularly suit him (co-ed, particular courses on offer, logistics etc) and I would recommend you include those in any appeal, rather than just relying on the glasses issue.
As for the glasses, you should try to gather evidence of this issue and to what extent it has affected him. So you will already have a prescription from the optician with a relevant date on it and I would keep that somewhere safe. If your optician is also willing to write a letter explaining in lay-man's terms the extent to which your DS would be disadvantaged in not wearing glasses that might also be helpful. But perhaps the best thing would be a letter from his school from the class-teacher or Head detailing any change / improvement in his work over the next few weeks/months after starting wearing them. So I would ask them to look out for any changes, saying you might want them to draft something in due course. What would be great of course would be if there were SATs levels pre and post glasses showing a huge difference in the before and after positions. As you are saying your son was level 5s at the end of Y5, it could be difficult to demonstrate much improvement. Some primary schools are happy to give level 6s, some aren't.
Hope that's food for thought. There is masses of really helpful info in the "Appeals" section you might want to look at. There, you'll see that it is difficult to predict who will win an appeal and who won't. Panels are made up of three individuals after all, and they have to assess your case in relation to the school's case and in relation to all the other appeals they hear that year. So there's no certainty in it, but it is worth going down the route if you strongly feel your DS would do better at a school other than the one he is allocated to.