All the seasons came with a bonus disk. This has nothing to do with any replacement discs, which is an entirely different matter.
There was one replacement disc that was offered when one of the seasons came out, but I want to say that it was the disc that has "Let He Who Is Without Sin..." on it. In some sets, that episode was not playable and Paramount gave us a phone number that we could call to get a replacement. But that was only for those who happened to get an unplayable disk. Anyway, if you had posted this in the DS9 forum, my peeps in there might have had more info. But that is what I remember, anyway. I know one Niner who is still here who got a replacement disk, and he might be able to help you with the specifics of that if you are interested. He might see this thread, but if he doesn't, his name is
Frontier.
The bonus disks were a different thing and came out in sets at the beginning. But I believe it was intended to be for a limited time. I don't think you can
expect the bonus discs anymore - if you got one, it's gravy. Or if you really want all of them, I'm sure you could get them on ebay...although likely some of them are fairly pricey.
By the way, the best one is the season 3 bonus disk as it has a special feature about the Defiant on it, with the best Ira Behr quote
ever - that the Defiant was "on a 5 year mission - to kick ass!"
Also of interest might be the fact that there were no bonus discs in R2 sets - all the stuff that was on R1 bonus discs came 'standard' in the R2 sets. So if you have a region free DVD player, it might be worth looking in to the R2 sets instead.