Until now I hadn't bothered trying Opus's folder size calculation against the test cycles I had created, as I assumed if you said there was a problem there was one (and it seemed reasonable that Opus didn't check for cycles as creating cycles seems wrong to me)...
But I just tried it anyway, to see what would happen. Opus seems to work fine for me; it stops counting when it hits the junction.
Here is the directory structure I created:
I created a cycle with both a junction and a softlink, in case there was a problem with one type and not the other.
As you can see, Opus's Flat View mode also knows to stop at a junction/link, and the folder size column only shows the size of File B.txt and has not recursed into the link or the junction.
This is using Opus 10.0.2.0 x64 on Windows 7.