The logo has been working its way onto all Spyderco blades over the last year or so. Not sure if they've kept track of when it was added to which model. As for your other question, with very few exceptions, any modification to a knife, or any visible signs of use, lower the "collector's value" to some exent. Most collectors want a knife in original, as manufactured, condition. So in that context, yes, polishing the blade would lower the value, whether or not the logo got removed in the process.
Frankly though, I think it will be a long time before any G-10 handled, VG-10 bladed, serrated edge Civilian will have "collector value" above street price. There are just too many of them. The only thing that would make the "bugged" version more valuable would be if Spydero were to discontinue the model, at the end of this year, making them a relatively rare variant. That, from what Sal said recently, is NOT going to happen.
On the other hand, some folks dislike "markings" of any kind on the blades of the carry pieces, and "may" be willing to pay a premium for one with no logo, or the logo removed. If that sounds like a waffle, it is, but it's the only honest answer.
