I was editing and I found an area with a lot of nodes with no tags, is there any reason not to delete them?
Probably not, the changeset I review dates from 2009, but better contact the user who made it.
In this case, it seems it was a bot. http://www.openstreetmap.org/user/woodpeck_fixbot
Maybe the same bot could fix this issue in a greater area.
I normaly load the area in JOSM, select all nodes (objects), run JOSM’s validation tool and remove all nodes without tags (and also fix other errors )
I would go with muralito. Although there is clearly an error here, it is possible that there is a deeper problem that needs investigating.
Please note that JOSM’s validator should normally only be used as a hint. Although nodes that have been present a long time and never tagged are probably safe to delete, in more general cases you need to know the area to understand whether there was a valid reason for the way it was tagged. Generally, if it were possible to fix a problem without thought, it would probably have been done mechanically, already.