I don't know if there is anything true to the silver screw mystique or not. I've owned several CE-2s, and the silver screw example on my board now is the best I've heard by a large margin. OTOH the CE-2 circuit is essentially the same throughout it's life, so maybe it's down to component tolerances and luck.
Regarding other pedals, I think it comes down to circuit revisions (or lack thereof) when determining if the MIJ or silver screw version is better than its counterpart. The DS-1 has been through several revisions, so it's probably true that the MIJ versions are better. The SD-1 circuit OTOH has never changed, so it's very unlikely that the MIJ version sounds different, let alone better. Two other pedals where I swear by the MIJ version are the DD-3 and CS-3. The MIJ DD-3 uses the "long chip" from the SDE-3000 rackmount delay, and it sounds indescribably better than the later version. The MIJ CS-3 uses a dbx VCA unlike the THAT Corp VCA in the later pedals. I don't know if there are any other circuit changes, but my MIJ CS-3 sounds great whereas all of the MIT versions I've played are rather uninspiring.