I see where you are coming from. Let's break things down a bit.
1) Find References Incrementally. Everything you have said indicates to me that you want this option OFF. So, let's not talk about it. You know what, I don't like this setting either, but it exists because we have users who prefer it, because they want to search for references and get back to the editor as soon as possible. Their philosophy is that they are going to be fed references one at a time when they hit next-ref (Ctrl+G), and they probably do not even look at the References tool window, so a bit of clutter means nothing.
2) ...NO REFERENCES. In either mode, if you manually click on a file to expand it, and the file has no references, instead of deleting the file from the list, we tag it with "...NO REFERENCES", and yes, it doesn't go away, and that is a bit annoying. The problem is we can't just delete it, it would be really, really confusing. Think through the use-case, you click on "UtilityFunction.h" to expand it, there are no references, and the node just disappears. You are left wondering what happened and unless you are really paying attention, you probably have already forgotten what file you clicked on, or maybe you didn't really click on anything at all. The evidence is gone. Maybe you wanted to specifically check if that file referenced your symbol. So, we leave the breadcrumb behind "...NO REFERENCES" so that you can clearly see what happened. We only do this when you manually click on a node to expand it. In other cases, we delete file nodes after we try to expand them and they have no contents. I am making a tweak to how it cleans itself up when you do a next-ref, so you'll see less "...NO REFERENCES" nodes in the case that you are searching incrementally, or you have interrupted the references search and you are effectively searching incrementally.
3) The long list of files. So, you have one of two options here, you just wait for references to finish vetting the list of files, or you interrupt it early. Note that when you interrupt references, you are effectively putting it in Incremental mode. The same is true when References hits its max-found limit (Tools > Options > Editing > Context Tagging(R) > Maximums > Maximum items found in references search). So what do we do then? We have this list of remaining files that might have references, or might not. You might know exactly where you want to look for references, so you can manually drill down on those files. That is very convenient. You say it is useless, but I think you are confusing what you know about your code with what SlickEdit has not had the opportunity to discover yet. It can't know a file has no references until it does the calculation, you might know it because you know your code.
4) Calculate refs up front. I can and will add this option. This discussion has given me an idea of how this can be done without taking a step backwards. It will require displaying a progress dialog, because it is really bad form to just have the editor sit there grinding for what could take minutes without a clear indication of a finish line and clear way to stop it. Also, if you cancel, you will be left with files that are unvetted and unexpanded, just like before. This option will be off by default, the existing system of calculating references in the background on a timer is superior, since you can keep working while the references get flushed out.