The 3D viewer doesn't "tent" vias, so what you see is perfectly normal (at least it works as intended). Stitching vias are just vias. Nothing special.
Now if you are expecting to see not tented (meaning covered by solder mask), but rather filled vias, I don't think that's supported by the 3D viewer, and not sure this is supported by KiCad in general either (AFAIK you can only set a via as blind, buried or through-hole at this point). If anyone knows how to explicitely set a via as filled in KiCad, please let me know.
And as whalphen said, not all PCB manufacturers can actually do that, and when they do, that can be a pretty expensive option. I'd suggest doing that only if you have a very good reason to, and then you'd have to instruct the manufacturer explicitely as it won't show in KiCad's output files (again AFAIK, if anyone knows how to, don't hesitate to mention it).