Indeed. We have to remember that Omega is a machine. Advanced beyond comprehension, but still a machine and does not possess a soul whose aether returns to the lifestream upon death as those on Hydaelyn know it. Much like a computer; we can smash it to bits, but if its memory is stored in a flash drive (OMG), then it is simple a matter of transferring it over to another computer. Fortunately, we don't have the technology to build Omega another 'body', but it is still there. Learning. Processing. It could be several millennia, but Omega's return is inevitable.
I really don't know how anything and everything that has to do with Omega cannot be considered canon. The raids themselves simply represent our encounters with it. Considering that Omega is mentioned in the early MSQ and seen as a great threat that is visibly witnessed at the end of HW, we can only assume that the absolute certain debriefing from the WoL and Ironworks of its defeat takes place off screen. There's just no way Nanamo and co. would just accept its no longer around without knowing how that came to be so.
As for the main topic. I seem to remember five weapons in total from VII. Three of them are part of the story, and two are super bosses that have nothing to do with the main story outside the lore. One of the three (Sapphire) gets its head blasted off while wrecking Junon, and we don't encounter it in battle. Another (Diamond), we encounter briefly before it marches off to Midgar and we see what happens in FMV when a tank buster isn't mitigated. The third is this weird version of Ultimate that is part of the main story, but it's not; it's also an optional boss, but it's not.
With at least seven trials per expansion that award mounts, weapons, and other valuable primal drops along with the exclusion of Ultimate, I'd imagine we are getting Ruby, Emerald, Diamond, and Sapphire. If so, it is interesting that they are starting off with Ruby. Perhaps Sapphire will get the love it was denied in VII. It will be interesting to see certain abilities from Ruby and Emerald modernized into mechanics for FFXIV and should be fun. Diamond and Sapphire though, they would have a lox of flexibility with how to create their encounters. Will have to see.