I JUST DISCOVERED SAME THING!!!! I can't find it again but I swear I had it say I had 1100 of them somewhere. How the hell does that happen and how do I batch delete them?
choose 'unused' selct one and then Ctrl-A (Select All shortcut)
That works for the instance on PC where I deleted almost everything already and the spacers ended up in the unused category.
That's not the case for my working instance on the Raspberry Pi where they seem to be under the ui_spacer group currently. Ive deleted all of my dashboard nodes but those dang spacers are still sitting there under the ui_spacer section taunting me. 
I went in and edited the JSON file in a text editor and deleted all of the rogue spacer nodes and that worked. Now, when I delete 20 or more nodes, they disappear in a couple of seconds which is reasonable based on the size of my instance and that I am running on a RPi 4.
Thank you to everyone who contributed to solving this bizarre issue. I wish I knew how I screwed it up in the first place. UGH!!!!! But, it's solved!! Thank you again to all!!!
I've found copy and pasting bits of flow, particularly when using the import function, dashboard nodes and other nodes that store things in config tend to duplicate their configurations whenever copied, but don't always get rid of them when deleted or modified. If your flows are as big as described, copying, changing and deleting a moderately complex dashboard flow a few times could well give you a bunch of left over bits.
I use the MSSQL nodes a lot, and every time they are imported they create another config with the same name as the ones I already have.
I don't think this issue is completely solved, I had this issue a few months ago found loads of unused spacer nodes I deleted them, it solved the problem, I put it down to my mistake, however upon reading this post I checked in 'configuration nodes' and there they are again about 100 of them, I checked my other pi's and they all have them to a varying degree one pi that I don't make many changes to has just 2 spurious spacers, obviously something is generating these nodes, but how to track down what's causing this ?
You are probably right that issue isn't solved in that the cause isn't fixed but at least I know what to look for and how to correct it. Now that I know about the spacers issue and have Googled it, I have found other posts where people have noticed same issue on a smaller scale when they have imported others' flows.
For duplicate configuration nodes, just look at the active links number. Then, consolidate, I have to do this often with MySQL nodes, after I have done importing of various flows to the same device.
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