Ofcourse, but there are alternatives for all of those.
I might have worded it incorrectly though, I don't think 5.25" bays are going to disappear completely. But I do think they will disappear on a lot of the more performance and/or space efficiency oriented case designs.
There will always be those cases with a few 5.25" bays, a massive amount of HDD trays, etc. But I think they're going to become more of a niche as time goes on.