Superman stories by Jerry Siegel continued to appear up until the end of 1947 (the last in World's Finest Comics 32 (Jan/Feb 1948), on sale November 28, 1947. During his war service, the number of stories went down, especially in 1945 when there seems to be only two. Shuster's eyesight was already failing when they first started Superman, which is why the other artists in his studio (under his management) did more and more of the art over the years. One source I checked says Joe also did military service, but it doesn't give details. I'll have to do some more digging, because it seems to me that with his eyesight Shuster should not have been in active service (although many have gotten into the military anyway, despite medical issues).
The first Superboy story, however, is credited to Jerry Siegel and Joe Shuster. The argument over Superboy is extremely complex and I can't remember the details off hand. The fact that Jerry was away in the military is part of the reason he said DC didn't have his permission to do Superboy. But I would have to do a lot more research to represent the full argument.