Thanks for the report. Can you send us one such effect at support _at_ popcornfx _dot_ com please?
This most likely comes from an editor bug that doesn't properly cleanup some of the child nodes when deleting something, we'll take a look.
But fixing this won't help with the effects that already contain garbage nodes, so maybe we can add something that cleans the effects and removes any unused node.
Regarding the node editor, it's a very old viewer that has been unmaintained for years (and terminally broken when deleting stuff, as you have experienced), and has been kept in for a handful of users that used it to customize some very specific stuff that will not exist anymore in v2.0. It's not meant to be used at all, in fact it should either be entirely removed, or the menu items to open it should only appear if launching the editor with a specific command-line, for those 2 or 3 users I mentioned.
I'll submit the idea for an upcoming patch.