I would try creating a new profile and testing with it. Or
http://www.winhelponline.com/blog/clear-customize-notifications-tray-items-windows-7-vista-xp/
you could use the script mentioned in the article and run it via task scheduler at whatever interval you need. Note please scan the script for malware before using it. Good luck
No, that script just clears the list of icons and their settings that Windows remembers. It's for people who don't like icons for things that never show up any more still being present in that option dialog. It has absolutely no bearing on OP's problem.
Anyway, when a program adds an icon to the system notification, that icon is created and owned by the Shell. And when you mouse over or otherwise interact with that icon, the Shell passes the message to the program that added the icon.
Now, when a program crashes, exits or otherwise terminates, all of its windows are automatically destroyed. But its notification area icons are not, because it doesn't technically actually own those icons. It's up to the Windows Shell to destroy them. And the Windows Shell destroys them when either the program tells the Shell to destroy the icon (which evidently is not happening here), or when the Shell tries to pass a message along to the program and finds that nobody's home.
Note that the Shell does
not check every x seconds to see if a program is alive or not because that's wasteful (waking up the process regularly is something you want to avoid), which is why these excess icons are removed only when you mouse over them--because that's when the Shell tries to notify the program that, "hey, someone just moused over your notification icon" and discovers that nobody's at the other end.
So programs that add icons to the system notification area need to tell the Shell to destroy the icon before they exit. As for why that's not happening, the most common cause is that the program crashed--i.e., it died before it had a chance to tell the Shell to clean up. Or there could be a bug in the program that results in this being bypassed somehow. It's an Opera problem, not a Windows problem.
It's unlikely that a new user profile will fix anything, and no, there isn't a way I know of to automate removing excess icons--because it's supposed to be a very rare thing. If you have that many, then there's something seriously wrong with your Opera.
