I never thought this would be an issue at all. The possibility to have multiple instances is one of the features in CE that I find really useful, and I often find myself using more than two instances. Can be a wee bit confusing at times, I admit, but nevertheless I keep on opening several CE instances. So please don't put a limit on the number of instances!
Oh, one thing: Make sure that the files that were open when the editor was shut down (i.e.: all instances closed) are opened only in the first instance, just the way CE does it.