UPDATE
I found out that the same ship, the Romulan Valdore class Warbird, has the same issue if you save it as a large design also.
So, after reading the posts, I tried out some stuff
I saved my game with a different name and reopened the new save using the cheat keys. Then I made new ship designs, two each for the Valdore class as both large and huge. One of each design had beam weapons only one at each hard point, while the second designs had mutiple beam weapons in one hard point using the ten-in-one cluster
I then tested them in battle. The designs that had just one weapon per hard point showed up just fine, while the mulitple ones didn't, so it seems like the clustering isn't working out.
So is there a way to fix this?