I have the owncloud client and the dropbox client installed and they're on the system tray. If I have them both set to hidden, when I click to show hidden icons and then try to click or right click on them, nothing happens. If I set them to Auto/Visible and they appear on the taskbar, I am able to right click or open them fine. I'm using KDE 4.10.2, and this didn't use to happen with older versions ( before the QML port I believe)

Can you check to see if the application menus are appearing beneath the system tray popup containing the hidden icons?
It is likely you are seeing bugs in the system tray functionality of these two applications here.

No. I have composting on, so the pop-up is transparent.

I can reproduce this with almost any non-kde tray icon that is set as hidden. Except Steam client, which actually gets a menu when right-clicking.

None of my bug reports ever get fixed, so I usually hope theres a work-around.

edit: Ahh, I find that the bug is already reported, but with an issue of the battery widget.

https://bugs.kde.org/show_bug.cgi?id=301424

Workaround seems that the text doesn't work, but the clicking on the icons do.

This is probably because "legacy" system tray icons such as those used by the Owncloud and Dropbox clients only acknowledge clicks on their icons - while Plasma can initiate events for new generation system tray icons, which is what KDE applications, and quite possibly the Steam client use.