If a file is opened using the command line, WebStorm/IDEA should check all of its windows to see if that file is open in any of them. If it is already open in an existing window then IDEA should bring window and the correct tab to the front.
Currently the IDEA only seems to check the last active window. So even if a file is already open in an existing tab in a second window, a new tab will be opened in the first.
Optimally, if the file isn't open in any of the windows, IDEA should scan the projects themselves to see if the file exists in any of the projects. If the file is in one of the existing projects, then the new tab should be opened in that project's window. In the rare case where a file exists in multiple projects, I would say it should just open in one of them.
I'll add that when IDEA has multiple projects/windows it's still a single process so it should be very doable to walk through all the window's tabs.
PS, If someone does work on tweaking this command line behavior, while you are in that bit of code it would be great if you could also look at adding a line number argument like I describe at http://devnet.jetbrains.net/thread/291600.