Interesting. I have seen single node objects now and then. But I have not seen a file with more than one or 2.
When you select them, does the status bar indicate any fill or stroke? Edit menu > Find might be able to select them all at once. I'd have to experiment to find out. Or you might be able to find the right configuration for the Find dialog, yourself. If you set it up right, you can use part of the XML, which you can get from the XML Editor.
If you could share the SVG file, I'd be glad to experiment. (It could take a long time to create a test file with more than one single node, haha.)
There's another relatively new way of selecting similar objects, which is Edit menu > Select Same. But I don't think it works by number of nodes. If all those single node objects have the same fill or stroke color, that are different from all the other objects, it would work.
There are some little known selection techniques which might be helpful. See the manual:
http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Select.html (Note that the Find dialog shown in that section is the old one - the new one can do a LOT more.)